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Conserved domains on  [gi|124430766|ref|NP_659122|]
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E3 ubiquitin-protein ligase UHRF2 isoform 1 [Mus musculus]

Protein Classification

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
TTD pfam12148
Tandem tudor domain within UHRF1; TTD, tandem tudor domain within UHRF1 preferentially binds ...
125-313 1.28e-85

Tandem tudor domain within UHRF1; TTD, tandem tudor domain within UHRF1 preferentially binds H3 histone tails trimethylated at Lys-9. It specifically recognizes H3 tail peptides with the heterochromatin-associated modification state of trimethylated lysine 9 and unmodified lysine 4 (H3K4me0/K9me3). This domain is found in eukaryotes and is found in association with pfam00097, pfam02182, pfam00628, pfam00240.


:

Pssm-ID: 432363 [Multi-domain]  Cd Length: 155  Bit Score: 268.33  E-value: 1.28e-85
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124430766  125 FGLYKVNELVDARDVGLGAWFEAHIHSVTRASDGHSrgktplkngssykrtngnvnhnskentnkldnvPSTSNSDSVAA 204
Cdd:pfam12148   1 KGLYKINELVDARDVSIGAWFEAKIVKVTKDKDSKD---------------------------------ESTSNSDSSTS 47
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124430766  205 DEDVIYHIEYDEYPESGILEMNVKDLRPRARTILKWNELNVGDVVMVNYNVENPGKRGFWYDAEITTLKTiSRTKKEVRV 284
Cdd:pfam12148  48 EEDVIYHVKYDDYPENGVVEMKLKDVRPRARTILKWDDLKVGQVVMVNYNPDEPKERGFWYDAEITEKKE-TRTSKELYG 126
                         170       180
                  ....*....|....*....|....*....
gi 124430766  285 KVFLGGSEGTLNDCRVMSVDEIFKIEKPG 313
Cdd:pfam12148 127 KILLGGDGDVLNDCKIKFVDEIFKIEEPG 155
SAD_SRA pfam02182
SAD/SRA domain; The domain goes by several names including SAD, SRA and YDG. It adopts a beta ...
447-615 4.11e-65

SAD/SRA domain; The domain goes by several names including SAD, SRA and YDG. It adopts a beta barrel, modified PUA-like, fold that is widely present in eukaryotic chromatin proteins and in bacteria. Versions of this domain are known to bind hemi-methylated CpG dinucleotides and also other 5mC containing dinucleotides. The domain binds DNA by flipping out the methylated cytosine base from the DNA double helix.The conserved tyrosine and aspartate residues and a glycine rich patch are critical for recognition of the flipped out base. Mammalian UHRF1 that contains this domain plays an important role in maintenance of methylation at CpG dinucleotides by recruiting DNMT1 to hemimethylated sites associated with replication forks. The SAD/SRA domain has been combined with other domains involved in the ubiquitin pathway on multiple occasions and such proteins link recognition of DNA methylation to chromatin-protein ubiquitination. The domain is also found in species that lack DNA methylation, such as certain apicomplexans, suggestive of other DNA-binding modes or functions. A highly derived and distinct version of the domain is also found in fungi where it is fused to AlkB-type 2OGFeDO domains. In bacteria, the domain is usually fused or associated with restriction endonucleases, many of which target methylated or hemi-methylated DNA.


:

Pssm-ID: 426640  Cd Length: 146  Bit Score: 213.56  E-value: 4.11e-65
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124430766  447 HYGPIPGIPVGSTWRFRVQVSEAGVHRPHVGGIHGRSNDGAYSLVLAGGFEDEVDRGDEFTYTGSGGKNLAGNKRigapS 526
Cdd:pfam02182   1 RFGHVPGVEVGDIFSSRAELCVVGLHRPTQAGIDGMKSEGAYSIVLSGGYEDDEDNGDVLIYTGSGGRDNTKKKQ----S 76
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124430766  527 ADQTLTNMNRALALNCdaplddkigaesrnwRAGKPVRVIRSFKGrkiSKYAPEEGNRYDGIYKVVKYWPEISSShGFLV 606
Cdd:pfam02182  77 ADQKLERGNLALANSC---------------ETGNPVRVIRGSKR---DSYPPKKGYRYDGLYKVEKYWEEKGKS-GFLV 137

                  ....*....
gi 124430766  607 WRYLLRRDD 615
Cdd:pfam02182 138 FKFKLRRLP 146
Ubl_UHRF2 cd17123
ubiquitin-like (Ubl) domain found in ubiquitin-like PHD and RING finger domain-containing ...
1-74 5.36e-45

ubiquitin-like (Ubl) domain found in ubiquitin-like PHD and RING finger domain-containing protein 2 (UHRF2); UHRF2, also termed Np95/ICBP90-like RING finger protein (NIRF), or Np95-likeRING finger protein, or nuclear protein 97, or nuclear zinc finger protein Np97, or RING finger protein 107, or E3 ubiquitin-protein ligase UHRF2, was originally identified as a ubiquitin ligase acting as a small ubiquitin-like modifier (SUMO) E3 ligase that enhances zinc finger protein 131(ZNF131) SUMOylation but does not enhance ZNF131 ubiquitination. It also ubiquitinates PCNP, a PEST-containing nuclear protein. Moreover, UHRF2 functions as a nuclear protein involved in cell-cycle regulation and has been implicated in tumorigenesis. It interacts with cyclins, CDKs, p53, pRB, PCNA, HDAC1, DNMTs, G9a, methylated histone H3 lysine 9, and methylated DNA. It interacts with the cyclin E-CDK2 complex, ubiquitinates cyclins D1 and E1, induces G1 arrest, and is involved in the G1/S transition regulation. Furthermore, UHRF2 is a direct transcriptional target of the transcription factor E2F-1 in the induction of apoptosis. It recruits HDAC1 and binds to methyl-CpG. UHRF2 also participates in the maturation of Hepatitis B virus (HBV) through interacting with HBV core protein and promoting its degradation. UHRF2 contains an N-terminal ubiquitin-like domain (Ubl), a tandem Tudor domain (TTD), a plant homeodomain (PHD) finger, a set- and ring-associated (SRA) domain, and a C-terminal RING finger.


:

Pssm-ID: 340643  Cd Length: 74  Bit Score: 155.41  E-value: 5.36e-45
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 124430766   1 MWIQVRTIDGSQTRTIEDVSRKATIEELRERVWALFDVRPECQRLFYRGKQLENGYTLFDYDVGLNDIIQLLVR 74
Cdd:cd17123    1 MWIQVRTIDGTETQTIDDLSRLTKIESLREKIQELFNVRPERQRLFYRGKQLEDGHTLFDYNVGLNDIVQLLIR 74
RING-HC_UHRF2 cd16770
RING finger, HC subclass, found in ubiquitin-like PHD and RING finger domain-containing ...
729-793 1.65e-39

RING finger, HC subclass, found in ubiquitin-like PHD and RING finger domain-containing protein 2 (UHRF2); UHRF2, also known as Np95/ICBP90-like RING finger protein (NIRF), Np95-like RING finger protein, nuclear protein 97, nuclear zinc finger protein Np97, RING finger protein 107, or E3 ubiquitin-protein ligase UHRF2, was originally identified as a ubiquitin ligase acting as a small ubiquitin-like modifier (SUMO) E3 ligase that enhances zinc finger protein 131 (ZNF131) SUMOylation, but does not enhance ZNF131 ubiquitination. It also ubiquitinates PCNP, a PEST-containing nuclear protein. Moreover, UHRF2 functions as a nuclear protein involved in cell-cycle regulation and has been implicated in tumorigenesis. It interacts with cyclins, CDKs, p53, pRB, PCNA, HDAC1, DNMTs, G9a, methylated histone H3 lysine 9, and methylated DNA. It interacts with the cyclin E-CDK2 complex, ubiquitinates cyclins D1 and E1, induces G1 arrest, and is involved in the G1/S transition regulation. Furthermore, UHRF2 is a direct transcriptional target of the transcription factor E2F-1 in the induction of apoptosis. It recruits HDAC1 and binds to methyl-CpG. UHRF2 also participates in the maturation of Hepatitis B virus (HBV) through interacting with HBV core protein and promoting its degradation. UHRF2 contains an N-terminal ubiquitin-like domain (UBL), a tandem Tudor domain (TTD), a plant homeodomain (PHD) domain, a SET- and RING-associated (SRA) domain, and a C-terminal C3HC4-type RING-HC finger.


:

Pssm-ID: 438426 [Multi-domain]  Cd Length: 65  Bit Score: 139.95  E-value: 1.65e-39
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 124430766 729 EQSFMCVCCQELVYQPVTTECFHNVCKDCLQRSFKAQVFSCPACRHDLGQNYVMVLNETLQTLLD 793
Cdd:cd16770    1 EESFLCICCQELVYQPVTTECQHNVCKSCLQRSFKAEVYTCPACRHDLGKNYSMVPNKILQTLLD 65
PHD_UHRF2 cd15617
PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein 2 (UHRF2); ...
347-393 3.87e-28

PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein 2 (UHRF2); UHRF2 (also termed Np95/ICBP90-like RING finger protein (NIRF), Np95-like RING finger protein, nuclear protein 97, nuclear zinc finger protein Np97, RING finger protein 107, or E3 ubiquitin-protein ligase UHRF2) was originally identified as a ubiquitin ligase acting as a small ubiquitin-like modifier (SUMO) E3 ligase that enhances zinc finger protein 131 (ZNF131) SUMOylation but does not enhance ZNF131 ubiquitination. It also ubiquitinates PCNP, a PEST-containing nuclear protein. Moreover, UHRF2 functions as a nuclear protein involved in cell-cycle regulation and has been implicated in tumorigenesis. It interacts with cyclins, CDKs,p53, pRB, PCNA, HDAC1, DNMTs, G9a, methylated histone H3 lysine 9, and methylated DNA. It interacts with the cyclin E-CDK2 complex, ubiquitinates cyclins D1 and E1, induces G1 arrest, and is involved in the G1/S transition regulation. Furthermore, UHRF2 is a direct transcriptional target of the transcription factor E2F-1 in the induction of apoptosis. It recruits HDAC1 and binds to methyl-CpG. UHRF2 also participates in the maturation of Hepatitis B virus (HBV) by interacting with the HBV core protein and promoting its degradation. UHRF2 contains an N-terminal ubiquitin-like domain (UBL), a tandem Tudor domain (TTD), a plant homeodomain (PHD) finger, a SET- and RING-associated (SRA) domain, and a C-terminal RING finger.


:

Pssm-ID: 277089  Cd Length: 47  Bit Score: 106.96  E-value: 3.87e-28
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 124430766 347 SCHKCGEKRDPNMQLLCDECNMAYHIYCLSPPLDKVPEEEYWYCPSC 393
Cdd:cd15617    1 SCYVCGGKQDAHMQLLCDECNMAYHIYCLNPPLDKIPEDEDWYCPSC 47
 
Name Accession Description Interval E-value
TTD pfam12148
Tandem tudor domain within UHRF1; TTD, tandem tudor domain within UHRF1 preferentially binds ...
125-313 1.28e-85

Tandem tudor domain within UHRF1; TTD, tandem tudor domain within UHRF1 preferentially binds H3 histone tails trimethylated at Lys-9. It specifically recognizes H3 tail peptides with the heterochromatin-associated modification state of trimethylated lysine 9 and unmodified lysine 4 (H3K4me0/K9me3). This domain is found in eukaryotes and is found in association with pfam00097, pfam02182, pfam00628, pfam00240.


Pssm-ID: 432363 [Multi-domain]  Cd Length: 155  Bit Score: 268.33  E-value: 1.28e-85
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124430766  125 FGLYKVNELVDARDVGLGAWFEAHIHSVTRASDGHSrgktplkngssykrtngnvnhnskentnkldnvPSTSNSDSVAA 204
Cdd:pfam12148   1 KGLYKINELVDARDVSIGAWFEAKIVKVTKDKDSKD---------------------------------ESTSNSDSSTS 47
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124430766  205 DEDVIYHIEYDEYPESGILEMNVKDLRPRARTILKWNELNVGDVVMVNYNVENPGKRGFWYDAEITTLKTiSRTKKEVRV 284
Cdd:pfam12148  48 EEDVIYHVKYDDYPENGVVEMKLKDVRPRARTILKWDDLKVGQVVMVNYNPDEPKERGFWYDAEITEKKE-TRTSKELYG 126
                         170       180
                  ....*....|....*....|....*....
gi 124430766  285 KVFLGGSEGTLNDCRVMSVDEIFKIEKPG 313
Cdd:pfam12148 127 KILLGGDGDVLNDCKIKFVDEIFKIEEPG 155
SAD_SRA pfam02182
SAD/SRA domain; The domain goes by several names including SAD, SRA and YDG. It adopts a beta ...
447-615 4.11e-65

SAD/SRA domain; The domain goes by several names including SAD, SRA and YDG. It adopts a beta barrel, modified PUA-like, fold that is widely present in eukaryotic chromatin proteins and in bacteria. Versions of this domain are known to bind hemi-methylated CpG dinucleotides and also other 5mC containing dinucleotides. The domain binds DNA by flipping out the methylated cytosine base from the DNA double helix.The conserved tyrosine and aspartate residues and a glycine rich patch are critical for recognition of the flipped out base. Mammalian UHRF1 that contains this domain plays an important role in maintenance of methylation at CpG dinucleotides by recruiting DNMT1 to hemimethylated sites associated with replication forks. The SAD/SRA domain has been combined with other domains involved in the ubiquitin pathway on multiple occasions and such proteins link recognition of DNA methylation to chromatin-protein ubiquitination. The domain is also found in species that lack DNA methylation, such as certain apicomplexans, suggestive of other DNA-binding modes or functions. A highly derived and distinct version of the domain is also found in fungi where it is fused to AlkB-type 2OGFeDO domains. In bacteria, the domain is usually fused or associated with restriction endonucleases, many of which target methylated or hemi-methylated DNA.


Pssm-ID: 426640  Cd Length: 146  Bit Score: 213.56  E-value: 4.11e-65
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124430766  447 HYGPIPGIPVGSTWRFRVQVSEAGVHRPHVGGIHGRSNDGAYSLVLAGGFEDEVDRGDEFTYTGSGGKNLAGNKRigapS 526
Cdd:pfam02182   1 RFGHVPGVEVGDIFSSRAELCVVGLHRPTQAGIDGMKSEGAYSIVLSGGYEDDEDNGDVLIYTGSGGRDNTKKKQ----S 76
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124430766  527 ADQTLTNMNRALALNCdaplddkigaesrnwRAGKPVRVIRSFKGrkiSKYAPEEGNRYDGIYKVVKYWPEISSShGFLV 606
Cdd:pfam02182  77 ADQKLERGNLALANSC---------------ETGNPVRVIRGSKR---DSYPPKKGYRYDGLYKVEKYWEEKGKS-GFLV 137

                  ....*....
gi 124430766  607 WRYLLRRDD 615
Cdd:pfam02182 138 FKFKLRRLP 146
SRA smart00466
SET and RING finger associated domain; Domain of unknown function in SET domain containing ...
444-615 3.95e-55

SET and RING finger associated domain; Domain of unknown function in SET domain containing proteins and in Deinococcus radiodurans DRA1533.


Pssm-ID: 197742  Cd Length: 155  Bit Score: 186.80  E-value: 3.95e-55
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124430766   444 PSNHYGPIPGIPVGSTWRFRVQVSEAGVHRPHVGGIHGRS----NDGAYSLVLAGGFEDEVDRGDEFTYTGSGgknlaGN 519
Cdd:smart00466   1 MKRIFGPVPGVEVGDIFFYRVELCLVGLHRPTQAGIDGLEsdegEPGATSVVSSGGYEDDTDDGDVLIYTGQG-----GR 75
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124430766   520 KRIGAPSADQTLTNMNRALALNCdaplddkigaesrnwRAGKPVRVIRSFKGRkiSKYAPEEGNRYDGIYKVVKYWPEIs 599
Cdd:smart00466  76 DMTHGQPEDQKLERGNLALEASC---------------RKGIPVRVVRGMKGY--SKYAPGKGYIYDGLYRIVDYWREV- 137
                          170
                   ....*....|....*.
gi 124430766   600 SSHGFLVWRYLLRRDD 615
Cdd:smart00466 138 GKSGFLVFKFKLVRIP 153
Tudor_UHRF2_rpt1 cd20456
first Tudor domain found in ubiquitin-like PHD and RING finger domain-containing protein 2 ...
112-238 1.74e-48

first Tudor domain found in ubiquitin-like PHD and RING finger domain-containing protein 2 (UHRF2) and similar proteins; UHRF2, also called Np95/ICBP90-like RING finger protein (NIRF), Np95-like RING finger protein, nuclear protein 97, nuclear zinc finger protein Np97, RING finger protein 107, or E3 ubiquitin-protein ligase UHRF2, was originally identified as a ubiquitin ligase acting as a small ubiquitin-like modifier (SUMO) E3 ligase that enhances zinc finger protein 131 (ZNF131) SUMOylation but does not enhance ZNF131 ubiquitination. It also ubiquitinates PCNP, a PEST-containing nuclear protein. UHRF2 also functions as a nuclear protein involved in cell-cycle regulation and has been implicated in tumorigenesis. It interacts with cyclins, CDKs, p53, pRB, PCNA, HDAC1, DNMTs, G9a, methylated histone H3 lysine 9, and methylated DNA. It interacts with the cyclin E-CDK2 complex, ubiquitinates cyclins D1 and E1, induces G1 arrest, and is involved in the G1/S transition regulation. Furthermore, UHRF2 is a direct transcriptional target of the transcription factor E2F-1 in the induction of apoptosis. It recruits HDAC1 and binds to methyl-CpG. UHRF2 also participates in the maturation of Hepatitis B virus (HBV) through interacting with HBV core protein and promoting its degradation. UHRF2 contains an N-terminal ubiquitin-like domain (UBL), a tandem Tudor domain (TTD), a plant homeodomain (PHD) domain, a SET- and RING-associated (SRA) domain, and a C-terminal RING finger domain. The model corresponds to the first Tudor domain. The tandem Tudor domain directs binding of UHRF to the heterochromatin mark histone H3K9me3.


Pssm-ID: 410527  Cd Length: 91  Bit Score: 165.79  E-value: 1.74e-48
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124430766 112 PSTSARTCLIDPGFGLYKVNELVDARDVGLGAWFEAHIHSVTRAsdghsrgktplkngssykrtngnvnhnskentnkld 191
Cdd:cd20456    1 PSTSARAFLIDPGIGIYKINELVDARDVSIGAWFEAHIENVTRA------------------------------------ 44
                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 124430766 192 NVPSTSNSDSVAADEDVIYHIEYDEYPESGILEMNVKDLRPRARTIL 238
Cdd:cd20456   45 STPSTSNSDCMDADEDVIYHIKYDDYPENGVVEMDTGNLRPRARTIL 91
Ubl_UHRF2 cd17123
ubiquitin-like (Ubl) domain found in ubiquitin-like PHD and RING finger domain-containing ...
1-74 5.36e-45

ubiquitin-like (Ubl) domain found in ubiquitin-like PHD and RING finger domain-containing protein 2 (UHRF2); UHRF2, also termed Np95/ICBP90-like RING finger protein (NIRF), or Np95-likeRING finger protein, or nuclear protein 97, or nuclear zinc finger protein Np97, or RING finger protein 107, or E3 ubiquitin-protein ligase UHRF2, was originally identified as a ubiquitin ligase acting as a small ubiquitin-like modifier (SUMO) E3 ligase that enhances zinc finger protein 131(ZNF131) SUMOylation but does not enhance ZNF131 ubiquitination. It also ubiquitinates PCNP, a PEST-containing nuclear protein. Moreover, UHRF2 functions as a nuclear protein involved in cell-cycle regulation and has been implicated in tumorigenesis. It interacts with cyclins, CDKs, p53, pRB, PCNA, HDAC1, DNMTs, G9a, methylated histone H3 lysine 9, and methylated DNA. It interacts with the cyclin E-CDK2 complex, ubiquitinates cyclins D1 and E1, induces G1 arrest, and is involved in the G1/S transition regulation. Furthermore, UHRF2 is a direct transcriptional target of the transcription factor E2F-1 in the induction of apoptosis. It recruits HDAC1 and binds to methyl-CpG. UHRF2 also participates in the maturation of Hepatitis B virus (HBV) through interacting with HBV core protein and promoting its degradation. UHRF2 contains an N-terminal ubiquitin-like domain (Ubl), a tandem Tudor domain (TTD), a plant homeodomain (PHD) finger, a set- and ring-associated (SRA) domain, and a C-terminal RING finger.


Pssm-ID: 340643  Cd Length: 74  Bit Score: 155.41  E-value: 5.36e-45
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 124430766   1 MWIQVRTIDGSQTRTIEDVSRKATIEELRERVWALFDVRPECQRLFYRGKQLENGYTLFDYDVGLNDIIQLLVR 74
Cdd:cd17123    1 MWIQVRTIDGTETQTIDDLSRLTKIESLREKIQELFNVRPERQRLFYRGKQLEDGHTLFDYNVGLNDIVQLLIR 74
RING-HC_UHRF2 cd16770
RING finger, HC subclass, found in ubiquitin-like PHD and RING finger domain-containing ...
729-793 1.65e-39

RING finger, HC subclass, found in ubiquitin-like PHD and RING finger domain-containing protein 2 (UHRF2); UHRF2, also known as Np95/ICBP90-like RING finger protein (NIRF), Np95-like RING finger protein, nuclear protein 97, nuclear zinc finger protein Np97, RING finger protein 107, or E3 ubiquitin-protein ligase UHRF2, was originally identified as a ubiquitin ligase acting as a small ubiquitin-like modifier (SUMO) E3 ligase that enhances zinc finger protein 131 (ZNF131) SUMOylation, but does not enhance ZNF131 ubiquitination. It also ubiquitinates PCNP, a PEST-containing nuclear protein. Moreover, UHRF2 functions as a nuclear protein involved in cell-cycle regulation and has been implicated in tumorigenesis. It interacts with cyclins, CDKs, p53, pRB, PCNA, HDAC1, DNMTs, G9a, methylated histone H3 lysine 9, and methylated DNA. It interacts with the cyclin E-CDK2 complex, ubiquitinates cyclins D1 and E1, induces G1 arrest, and is involved in the G1/S transition regulation. Furthermore, UHRF2 is a direct transcriptional target of the transcription factor E2F-1 in the induction of apoptosis. It recruits HDAC1 and binds to methyl-CpG. UHRF2 also participates in the maturation of Hepatitis B virus (HBV) through interacting with HBV core protein and promoting its degradation. UHRF2 contains an N-terminal ubiquitin-like domain (UBL), a tandem Tudor domain (TTD), a plant homeodomain (PHD) domain, a SET- and RING-associated (SRA) domain, and a C-terminal C3HC4-type RING-HC finger.


Pssm-ID: 438426 [Multi-domain]  Cd Length: 65  Bit Score: 139.95  E-value: 1.65e-39
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 124430766 729 EQSFMCVCCQELVYQPVTTECFHNVCKDCLQRSFKAQVFSCPACRHDLGQNYVMVLNETLQTLLD 793
Cdd:cd16770    1 EESFLCICCQELVYQPVTTECQHNVCKSCLQRSFKAEVYTCPACRHDLGKNYSMVPNKILQTLLD 65
PHD_UHRF2 cd15617
PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein 2 (UHRF2); ...
347-393 3.87e-28

PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein 2 (UHRF2); UHRF2 (also termed Np95/ICBP90-like RING finger protein (NIRF), Np95-like RING finger protein, nuclear protein 97, nuclear zinc finger protein Np97, RING finger protein 107, or E3 ubiquitin-protein ligase UHRF2) was originally identified as a ubiquitin ligase acting as a small ubiquitin-like modifier (SUMO) E3 ligase that enhances zinc finger protein 131 (ZNF131) SUMOylation but does not enhance ZNF131 ubiquitination. It also ubiquitinates PCNP, a PEST-containing nuclear protein. Moreover, UHRF2 functions as a nuclear protein involved in cell-cycle regulation and has been implicated in tumorigenesis. It interacts with cyclins, CDKs,p53, pRB, PCNA, HDAC1, DNMTs, G9a, methylated histone H3 lysine 9, and methylated DNA. It interacts with the cyclin E-CDK2 complex, ubiquitinates cyclins D1 and E1, induces G1 arrest, and is involved in the G1/S transition regulation. Furthermore, UHRF2 is a direct transcriptional target of the transcription factor E2F-1 in the induction of apoptosis. It recruits HDAC1 and binds to methyl-CpG. UHRF2 also participates in the maturation of Hepatitis B virus (HBV) by interacting with the HBV core protein and promoting its degradation. UHRF2 contains an N-terminal ubiquitin-like domain (UBL), a tandem Tudor domain (TTD), a plant homeodomain (PHD) finger, a SET- and RING-associated (SRA) domain, and a C-terminal RING finger.


Pssm-ID: 277089  Cd Length: 47  Bit Score: 106.96  E-value: 3.87e-28
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 124430766 347 SCHKCGEKRDPNMQLLCDECNMAYHIYCLSPPLDKVPEEEYWYCPSC 393
Cdd:cd15617    1 SCYVCGGKQDAHMQLLCDECNMAYHIYCLNPPLDKIPEDEDWYCPSC 47
ubiquitin pfam00240
Ubiquitin family; This family contains a number of ubiquitin-like proteins: SUMO (smt3 homolog) ...
3-76 3.83e-14

Ubiquitin family; This family contains a number of ubiquitin-like proteins: SUMO (smt3 homolog), Nedd8, Elongin B, Rub1, and Parkin. A number of them are thought to carry a distinctive five-residue motif termed the proteasome-interacting motif (PIM), which may have a biologically significant role in protein delivery to proteasomes and recruitment of proteasomes to transcription sites.


Pssm-ID: 425549 [Multi-domain]  Cd Length: 72  Bit Score: 67.97  E-value: 3.83e-14
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 124430766    3 IQVRTIDGSQTrTIEdVSRKATIEELRERVWALFDVRPECQRLFYRGKQLENGYTLFDYDVGLNDIIQLLVRPD 76
Cdd:pfam00240   1 ITVKTLDGKKI-TLE-VDPTDTVLELKEKIAEKEGVPPEQQRLIYSGKVLEDDQTLGEYGIEDGSTIHLVLRQR 72
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
348-393 4.51e-11

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: 58.38  E-value: 4.51e-11
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 124430766   348 CHKCGEKRDPNMQLLCDECNMAYHIYCLSPPLDKVPEEEYWYCPSC 393
Cdd:smart00249   2 CSVCGKPDDGGELLQCDGCDRWYHQTCLGPPLLEEEPDGKWYCPKC 47
PHD pfam00628
PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...
348-394 5.13e-11

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: 58.27  E-value: 5.13e-11
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 124430766  348 CHKCGEKRDPNMQLLCDECNMAYHIYCLSPPLDKVPE-EEYWYCPSCK 394
Cdd:pfam00628   2 CAVCGKSDDGGELVQCDGCDDWFHLACLGPPLDPAEIpSGEWLCPECK 49
UBQ smart00213
Ubiquitin homologues; Ubiquitin-mediated proteolysis is involved in the regulated turnover of ...
3-74 9.68e-10

Ubiquitin homologues; Ubiquitin-mediated proteolysis is involved in the regulated turnover of proteins required for controlling cell cycle progression


Pssm-ID: 214563 [Multi-domain]  Cd Length: 72  Bit Score: 55.34  E-value: 9.68e-10
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 124430766     3 IQVRTIDGSqTRTIEdVSRKATIEELRERVWALFDVRPECQRLFYRGKQLENGYTLFDYDVGLNDIIQLLVR 74
Cdd:smart00213   3 LTVKTLDGK-TITLE-VKPSDTVSELKEKIAELTGIPPEQQRLIYKGKVLEDDRTLADYGIQDGSTIHLVLR 72
RING smart00184
Ring finger; E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and ...
734-772 1.23e-06

Ring finger; E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s)


Pssm-ID: 214546 [Multi-domain]  Cd Length: 40  Bit Score: 45.58  E-value: 1.23e-06
                           10        20        30
                   ....*....|....*....|....*....|....*....
gi 124430766   734 CVCCQELVYQPVTTECFHNVCKDCLQRSFKAQVFSCPAC 772
Cdd:smart00184   2 PICLEEYLKDPVILPCGHTFCRSCIRKWLESGNNTCPIC 40
zf-C3HC4 pfam00097
Zinc finger, C3HC4 type (RING finger); The C3HC4 type zinc-finger (RING finger) is a ...
734-772 4.87e-05

Zinc finger, C3HC4 type (RING finger); The C3HC4 type zinc-finger (RING finger) is a cysteine-rich domain of 40 to 60 residues that coordinates two zinc ions, and has the consensus sequence: C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C where X is any amino acid. Many proteins containing a RING finger play a key role in the ubiquitination pathway.


Pssm-ID: 395049 [Multi-domain]  Cd Length: 40  Bit Score: 41.19  E-value: 4.87e-05
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 124430766  734 CVCCQELVYQPVTTECFHNVCKDCLQRSFKAQVFSCPAC 772
Cdd:pfam00097   2 PICLEEPKDPVTLLPCGHLFCSKCIRSWLESGNVTCPLC 40
rad18 TIGR00599
DNA repair protein rad18; All proteins in this family for which functions are known are ...
725-773 5.40e-05

DNA repair protein rad18; All proteins in this family for which functions are known are involved in nucleotide excision repair.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273165 [Multi-domain]  Cd Length: 397  Bit Score: 46.15  E-value: 5.40e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 124430766  725 LKKLEQSFMCVCCQELVYQPVTTECFHNVCKDCLQRSFKAQVfSCPACR 773
Cdd:TIGR00599  20 LYPLDTSLRCHICKDFFDVPVLTSCSHTFCSLCIRRCLSNQP-KCPLCR 67
RAD18 COG5432
RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms];
725-775 6.31e-05

RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms];


Pssm-ID: 227719 [Multi-domain]  Cd Length: 391  Bit Score: 46.23  E-value: 6.31e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 124430766 725 LKKLEQSFMCVCCQELVYQPVTTECFHNVCKDCLQRSFKAQVFsCPACRHD 775
Cdd:COG5432   19 LKGLDSMLRCRICDCRISIPCETTCGHTFCSLCIRRHLGTQPF-CPVCRED 68
COG3440 COG3440
Predicted restriction endonuclease [Defense mechanisms];
447-619 9.86e-04

Predicted restriction endonuclease [Defense mechanisms];


Pssm-ID: 225973 [Multi-domain]  Cd Length: 301  Bit Score: 42.11  E-value: 9.86e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124430766 447 HYGPIPGIPVGSTWRFRVQVSEAGVHRPHVGGIHGRSNDGAYSLVLAGGFEDEVDRGDEFTYTGSGGKNLAGnkRIGAPs 526
Cdd:COG3440    5 NYYAKSFSQRNASLKIFGGNREAAPHKPILLLDVGRKISTFFITENQGIYETELIEPFIQLWSFFGPKLQKY--GVDAP- 81
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124430766 527 adQTLTNMNRALALNCDAPLDDkigaesrnwragkpvRVIRSFkgRKISKYAPEEGNRYDGIYKVVKYWPEISSSHgFLV 606
Cdd:COG3440   82 --FELLQGDGKWHLDIKEGFDG---------------LSIRTL--PTEKEFVEYHYIDDELEQSLQYHQGEKRLID-DLI 141
                        170
                 ....*....|....*
gi 124430766 607 WRYLLRR--DDVEPA 619
Cdd:COG3440  142 SIWRKEVlqEDIEEL 156
 
Name Accession Description Interval E-value
TTD pfam12148
Tandem tudor domain within UHRF1; TTD, tandem tudor domain within UHRF1 preferentially binds ...
125-313 1.28e-85

Tandem tudor domain within UHRF1; TTD, tandem tudor domain within UHRF1 preferentially binds H3 histone tails trimethylated at Lys-9. It specifically recognizes H3 tail peptides with the heterochromatin-associated modification state of trimethylated lysine 9 and unmodified lysine 4 (H3K4me0/K9me3). This domain is found in eukaryotes and is found in association with pfam00097, pfam02182, pfam00628, pfam00240.


Pssm-ID: 432363 [Multi-domain]  Cd Length: 155  Bit Score: 268.33  E-value: 1.28e-85
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124430766  125 FGLYKVNELVDARDVGLGAWFEAHIHSVTRASDGHSrgktplkngssykrtngnvnhnskentnkldnvPSTSNSDSVAA 204
Cdd:pfam12148   1 KGLYKINELVDARDVSIGAWFEAKIVKVTKDKDSKD---------------------------------ESTSNSDSSTS 47
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124430766  205 DEDVIYHIEYDEYPESGILEMNVKDLRPRARTILKWNELNVGDVVMVNYNVENPGKRGFWYDAEITTLKTiSRTKKEVRV 284
Cdd:pfam12148  48 EEDVIYHVKYDDYPENGVVEMKLKDVRPRARTILKWDDLKVGQVVMVNYNPDEPKERGFWYDAEITEKKE-TRTSKELYG 126
                         170       180
                  ....*....|....*....|....*....
gi 124430766  285 KVFLGGSEGTLNDCRVMSVDEIFKIEKPG 313
Cdd:pfam12148 127 KILLGGDGDVLNDCKIKFVDEIFKIEEPG 155
SAD_SRA pfam02182
SAD/SRA domain; The domain goes by several names including SAD, SRA and YDG. It adopts a beta ...
447-615 4.11e-65

SAD/SRA domain; The domain goes by several names including SAD, SRA and YDG. It adopts a beta barrel, modified PUA-like, fold that is widely present in eukaryotic chromatin proteins and in bacteria. Versions of this domain are known to bind hemi-methylated CpG dinucleotides and also other 5mC containing dinucleotides. The domain binds DNA by flipping out the methylated cytosine base from the DNA double helix.The conserved tyrosine and aspartate residues and a glycine rich patch are critical for recognition of the flipped out base. Mammalian UHRF1 that contains this domain plays an important role in maintenance of methylation at CpG dinucleotides by recruiting DNMT1 to hemimethylated sites associated with replication forks. The SAD/SRA domain has been combined with other domains involved in the ubiquitin pathway on multiple occasions and such proteins link recognition of DNA methylation to chromatin-protein ubiquitination. The domain is also found in species that lack DNA methylation, such as certain apicomplexans, suggestive of other DNA-binding modes or functions. A highly derived and distinct version of the domain is also found in fungi where it is fused to AlkB-type 2OGFeDO domains. In bacteria, the domain is usually fused or associated with restriction endonucleases, many of which target methylated or hemi-methylated DNA.


Pssm-ID: 426640  Cd Length: 146  Bit Score: 213.56  E-value: 4.11e-65
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124430766  447 HYGPIPGIPVGSTWRFRVQVSEAGVHRPHVGGIHGRSNDGAYSLVLAGGFEDEVDRGDEFTYTGSGGKNLAGNKRigapS 526
Cdd:pfam02182   1 RFGHVPGVEVGDIFSSRAELCVVGLHRPTQAGIDGMKSEGAYSIVLSGGYEDDEDNGDVLIYTGSGGRDNTKKKQ----S 76
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124430766  527 ADQTLTNMNRALALNCdaplddkigaesrnwRAGKPVRVIRSFKGrkiSKYAPEEGNRYDGIYKVVKYWPEISSShGFLV 606
Cdd:pfam02182  77 ADQKLERGNLALANSC---------------ETGNPVRVIRGSKR---DSYPPKKGYRYDGLYKVEKYWEEKGKS-GFLV 137

                  ....*....
gi 124430766  607 WRYLLRRDD 615
Cdd:pfam02182 138 FKFKLRRLP 146
SRA smart00466
SET and RING finger associated domain; Domain of unknown function in SET domain containing ...
444-615 3.95e-55

SET and RING finger associated domain; Domain of unknown function in SET domain containing proteins and in Deinococcus radiodurans DRA1533.


Pssm-ID: 197742  Cd Length: 155  Bit Score: 186.80  E-value: 3.95e-55
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124430766   444 PSNHYGPIPGIPVGSTWRFRVQVSEAGVHRPHVGGIHGRS----NDGAYSLVLAGGFEDEVDRGDEFTYTGSGgknlaGN 519
Cdd:smart00466   1 MKRIFGPVPGVEVGDIFFYRVELCLVGLHRPTQAGIDGLEsdegEPGATSVVSSGGYEDDTDDGDVLIYTGQG-----GR 75
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124430766   520 KRIGAPSADQTLTNMNRALALNCdaplddkigaesrnwRAGKPVRVIRSFKGRkiSKYAPEEGNRYDGIYKVVKYWPEIs 599
Cdd:smart00466  76 DMTHGQPEDQKLERGNLALEASC---------------RKGIPVRVVRGMKGY--SKYAPGKGYIYDGLYRIVDYWREV- 137
                          170
                   ....*....|....*.
gi 124430766   600 SSHGFLVWRYLLRRDD 615
Cdd:smart00466 138 GKSGFLVFKFKLVRIP 153
Tudor_UHRF2_rpt1 cd20456
first Tudor domain found in ubiquitin-like PHD and RING finger domain-containing protein 2 ...
112-238 1.74e-48

first Tudor domain found in ubiquitin-like PHD and RING finger domain-containing protein 2 (UHRF2) and similar proteins; UHRF2, also called Np95/ICBP90-like RING finger protein (NIRF), Np95-like RING finger protein, nuclear protein 97, nuclear zinc finger protein Np97, RING finger protein 107, or E3 ubiquitin-protein ligase UHRF2, was originally identified as a ubiquitin ligase acting as a small ubiquitin-like modifier (SUMO) E3 ligase that enhances zinc finger protein 131 (ZNF131) SUMOylation but does not enhance ZNF131 ubiquitination. It also ubiquitinates PCNP, a PEST-containing nuclear protein. UHRF2 also functions as a nuclear protein involved in cell-cycle regulation and has been implicated in tumorigenesis. It interacts with cyclins, CDKs, p53, pRB, PCNA, HDAC1, DNMTs, G9a, methylated histone H3 lysine 9, and methylated DNA. It interacts with the cyclin E-CDK2 complex, ubiquitinates cyclins D1 and E1, induces G1 arrest, and is involved in the G1/S transition regulation. Furthermore, UHRF2 is a direct transcriptional target of the transcription factor E2F-1 in the induction of apoptosis. It recruits HDAC1 and binds to methyl-CpG. UHRF2 also participates in the maturation of Hepatitis B virus (HBV) through interacting with HBV core protein and promoting its degradation. UHRF2 contains an N-terminal ubiquitin-like domain (UBL), a tandem Tudor domain (TTD), a plant homeodomain (PHD) domain, a SET- and RING-associated (SRA) domain, and a C-terminal RING finger domain. The model corresponds to the first Tudor domain. The tandem Tudor domain directs binding of UHRF to the heterochromatin mark histone H3K9me3.


Pssm-ID: 410527  Cd Length: 91  Bit Score: 165.79  E-value: 1.74e-48
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124430766 112 PSTSARTCLIDPGFGLYKVNELVDARDVGLGAWFEAHIHSVTRAsdghsrgktplkngssykrtngnvnhnskentnkld 191
Cdd:cd20456    1 PSTSARAFLIDPGIGIYKINELVDARDVSIGAWFEAHIENVTRA------------------------------------ 44
                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 124430766 192 NVPSTSNSDSVAADEDVIYHIEYDEYPESGILEMNVKDLRPRARTIL 238
Cdd:cd20456   45 STPSTSNSDCMDADEDVIYHIKYDDYPENGVVEMDTGNLRPRARTIL 91
Ubl_UHRF2 cd17123
ubiquitin-like (Ubl) domain found in ubiquitin-like PHD and RING finger domain-containing ...
1-74 5.36e-45

ubiquitin-like (Ubl) domain found in ubiquitin-like PHD and RING finger domain-containing protein 2 (UHRF2); UHRF2, also termed Np95/ICBP90-like RING finger protein (NIRF), or Np95-likeRING finger protein, or nuclear protein 97, or nuclear zinc finger protein Np97, or RING finger protein 107, or E3 ubiquitin-protein ligase UHRF2, was originally identified as a ubiquitin ligase acting as a small ubiquitin-like modifier (SUMO) E3 ligase that enhances zinc finger protein 131(ZNF131) SUMOylation but does not enhance ZNF131 ubiquitination. It also ubiquitinates PCNP, a PEST-containing nuclear protein. Moreover, UHRF2 functions as a nuclear protein involved in cell-cycle regulation and has been implicated in tumorigenesis. It interacts with cyclins, CDKs, p53, pRB, PCNA, HDAC1, DNMTs, G9a, methylated histone H3 lysine 9, and methylated DNA. It interacts with the cyclin E-CDK2 complex, ubiquitinates cyclins D1 and E1, induces G1 arrest, and is involved in the G1/S transition regulation. Furthermore, UHRF2 is a direct transcriptional target of the transcription factor E2F-1 in the induction of apoptosis. It recruits HDAC1 and binds to methyl-CpG. UHRF2 also participates in the maturation of Hepatitis B virus (HBV) through interacting with HBV core protein and promoting its degradation. UHRF2 contains an N-terminal ubiquitin-like domain (Ubl), a tandem Tudor domain (TTD), a plant homeodomain (PHD) finger, a set- and ring-associated (SRA) domain, and a C-terminal RING finger.


Pssm-ID: 340643  Cd Length: 74  Bit Score: 155.41  E-value: 5.36e-45
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 124430766   1 MWIQVRTIDGSQTRTIEDVSRKATIEELRERVWALFDVRPECQRLFYRGKQLENGYTLFDYDVGLNDIIQLLVR 74
Cdd:cd17123    1 MWIQVRTIDGTETQTIDDLSRLTKIESLREKIQELFNVRPERQRLFYRGKQLEDGHTLFDYNVGLNDIVQLLIR 74
Tudor_UHRF2_rpt2 cd20458
second Tudor domain found in ubiquitin-like PHD and RING finger domain-containing protein 2 ...
240-312 1.21e-41

second Tudor domain found in ubiquitin-like PHD and RING finger domain-containing protein 2 (UHRF2) and similar proteins; UHRF2, also called Np95/ICBP90-like RING finger protein (NIRF), Np95-like RING finger protein, nuclear protein 97, nuclear zinc finger protein Np97, RING finger protein 107, or E3 ubiquitin-protein ligase UHRF2, was originally identified as a ubiquitin ligase acting as a small ubiquitin-like modifier (SUMO) E3 ligase that enhances zinc finger protein 131 (ZNF131) SUMOylation but does not enhance ZNF131 ubiquitination. It also ubiquitinates PCNP, a PEST-containing nuclear protein. UHRF2 also functions as a nuclear protein involved in cell-cycle regulation and has been implicated in tumorigenesis. It interacts with cyclins, CDKs, p53, pRB, PCNA, HDAC1, DNMTs, G9a, methylated histone H3 lysine 9, and methylated DNA. It interacts with the cyclin E-CDK2 complex, ubiquitinates cyclins D1 and E1, induces G1 arrest, and is involved in the G1/S transition regulation. Furthermore, UHRF2 is a direct transcriptional target of the transcription factor E2F-1 in the induction of apoptosis. It recruits HDAC1 and binds to methyl-CpG. UHRF2 also participates in the maturation of Hepatitis B virus (HBV) through interacting with HBV core protein and promoting its degradation. UHRF2 contains an N-terminal ubiquitin-like domain (UBL), a tandem Tudor domain (TTD), a plant homeodomain (PHD) domain, a SET- and RING-associated (SRA) domain, and a C-terminal RING finger domain. The model corresponds to the second Tudor domain. The tandem Tudor domain directs binding of UHRF to the heterochromatin mark histone H3K9me3.


Pssm-ID: 410529  Cd Length: 73  Bit Score: 146.11  E-value: 1.21e-41
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 124430766 240 WNELNVGDVVMVNYNVENPGKRGFWYDAEITTLKTISRTKKEVRVKVFLGGSEGTLNDCRVMSVDEIFKIEKP 312
Cdd:cd20458    1 WNELKVGDVVMVNYNVETPEERGFWFDAEITTLKEISRTNKEVRVKILLGGPEDVINDCKILFLDEIYKIEKP 73
Ubl_UHRF cd01797
ubiquitin-like (Ubl) domain found in ubiquitin-like PHD and RING finger domain-containing ...
1-74 1.79e-41

ubiquitin-like (Ubl) domain found in ubiquitin-like PHD and RING finger domain-containing proteins, UHRF1 and UHRF2, and similar proteins; UHRF1 is a unique chromatin effector protein that integrates the recognition of both histone PTMs and DNA methylation. It is essential for cell proliferation and plays a critical role in the development and progression of many human carcinomas, such as laryngeal squamous cell carcinoma, gastric cancer, esophageal squamous cell carcinoma, colorectal cancer, prostate cancer, and breast cancer. UHRF1 can acts as a transcriptional repressor through its binding to histone H3 when it is unmodified at Arg2. Its overexpression in human lung fibroblasts results in downregulation of expression of the tumor suppressor pRB. It also plays a role in transcriptional repression of the cell cycle regulator p21. Moreover, UHRF1-dependent repression of factors can facilitate the G1-S transition. It interacts with Tat-interacting protein of 60 kDa (TIP60) and induces degradation-independent ubiquitination of TIP60. It is also an N-methylpurine DNA glycosylase (MPG)-interacting protein that binds MPG in a p53 status-independent manner in the DNA base excision repair (BER) pathway. In addition, UHRF1 functions as an epigenetic regulator that is important for multiple aspects of epigenetic regulation, including maintenance of DNA methylation patterns and recognition of various histone modifications. UHRF2 was originally identified as a ubiquitin ligase acting as a small ubiquitin-like modifier (SUMO) E3 ligase that enhances zinc finger protein 131 (ZNF131) SUMOylation but does not enhance ZNF131 ubiquitination. It also ubiquitinates PCNP, a PEST-containing nuclear protein. Moreover, UHRF2 functions as a nuclear protein involved in cell-cycle regulation and has been implicated in tumorigenesis. It interacts with cyclins, CDKs, p53, pRB, PCNA, HDAC1, DNMTs, G9a, methylated histone H3 lysine 9, and methylated DNA. It interacts with the cyclin E-CDK2 complex, ubiquitinates cyclins D1 and E1, induces G1 arrest, and is involved in the G1/S transition regulation. Furthermore, UHRF2 is a direct transcriptional target of the transcription factor E2F-1 in the induction of apoptosis. It recruits HDAC1 and binds to methyl-CpG. UHRF2 also participates in the maturation of Hepatitis B virus (HBV) through interacting with HBV core protein and promoting its degradation. Both UHRF1 and UHRF2 contain an N-terminal ubiquitin-like domain (Ubl), a tandem Tudor domain (TTD), a plant homeodomain (PHD) finger, a set- and ring-associated (SRA) domain, and a C-terminal RING finger.


Pssm-ID: 340495  Cd Length: 74  Bit Score: 145.59  E-value: 1.79e-41
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 124430766   1 MWIQVRTIDGSQTRTIEDVSRKATIEELRERVWALFDVRPECQRLFYRGKQLENGYTLFDYDVGLNDIIQLLVR 74
Cdd:cd01797    1 MWIQVRTMDGKKEARVDGLSKLTKIEDLRERIEEKFDVEPELQRLFYRGKQLEDGHTLFDYDVGLNDIIQLMVR 74
RING-HC_UHRF2 cd16770
RING finger, HC subclass, found in ubiquitin-like PHD and RING finger domain-containing ...
729-793 1.65e-39

RING finger, HC subclass, found in ubiquitin-like PHD and RING finger domain-containing protein 2 (UHRF2); UHRF2, also known as Np95/ICBP90-like RING finger protein (NIRF), Np95-like RING finger protein, nuclear protein 97, nuclear zinc finger protein Np97, RING finger protein 107, or E3 ubiquitin-protein ligase UHRF2, was originally identified as a ubiquitin ligase acting as a small ubiquitin-like modifier (SUMO) E3 ligase that enhances zinc finger protein 131 (ZNF131) SUMOylation, but does not enhance ZNF131 ubiquitination. It also ubiquitinates PCNP, a PEST-containing nuclear protein. Moreover, UHRF2 functions as a nuclear protein involved in cell-cycle regulation and has been implicated in tumorigenesis. It interacts with cyclins, CDKs, p53, pRB, PCNA, HDAC1, DNMTs, G9a, methylated histone H3 lysine 9, and methylated DNA. It interacts with the cyclin E-CDK2 complex, ubiquitinates cyclins D1 and E1, induces G1 arrest, and is involved in the G1/S transition regulation. Furthermore, UHRF2 is a direct transcriptional target of the transcription factor E2F-1 in the induction of apoptosis. It recruits HDAC1 and binds to methyl-CpG. UHRF2 also participates in the maturation of Hepatitis B virus (HBV) through interacting with HBV core protein and promoting its degradation. UHRF2 contains an N-terminal ubiquitin-like domain (UBL), a tandem Tudor domain (TTD), a plant homeodomain (PHD) domain, a SET- and RING-associated (SRA) domain, and a C-terminal C3HC4-type RING-HC finger.


Pssm-ID: 438426 [Multi-domain]  Cd Length: 65  Bit Score: 139.95  E-value: 1.65e-39
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 124430766 729 EQSFMCVCCQELVYQPVTTECFHNVCKDCLQRSFKAQVFSCPACRHDLGQNYVMVLNETLQTLLD 793
Cdd:cd16770    1 EESFLCICCQELVYQPVTTECQHNVCKSCLQRSFKAEVYTCPACRHDLGKNYSMVPNKILQTLLD 65
RING-HC_UHRF1 cd16769
RING finger, HC subclass, found in ubiquitin-like PHD and RING finger domain-containing ...
720-803 7.80e-38

RING finger, HC subclass, found in ubiquitin-like PHD and RING finger domain-containing protein 1 (UHRF1); UHRF1, also known as inverted CCAAT box-binding protein of 90 kDa, nuclear protein 95, nuclear zinc finger protein Np95 (Np95), RING finger protein 106, transcription factor ICBP90, or E3 ubiquitin-protein ligase UHRF1, is a unique chromatin effector protein that integrates the recognition of both histone PTMs and DNA methylation. It is essential for cell proliferation and plays a critical role in the development and progression of many human carcinomas, such as laryngeal squamous cell carcinoma (LSCC), gastric cancer (GC), esophageal squamous cell carcinoma (ESCC), colorectal cancer, prostate cancer, and breast cancer. UHRF1 can acts as a transcriptional repressor through its binding to histone H3 when it is unmodified at Arg2. Its overexpression in human lung fibroblasts results in downregulation of expression of the tumor suppressor pRB. It also plays a role in transcriptional repression of the cell cycle regulator p21. Moreover, UHRF1-dependent repression of factors can facilitate the G1-S transition. It interacts with Tat-interacting protein of 60 kDa (TIP60) and induces degradation-independent ubiquitination of TIP60. It is also a N-methylpurine DNA glycosylase (MPG)-interacting protein that binds MPG in a p53 status-independent manner in the DNA base excision repair (BER) pathway. In addition, UHRF1 functions as an epigenetic regulator that is important for multiple aspects of epigenetic regulation, including maintenance of DNA methylation patterns and recognition of various histone modifications. UHRF1 contains an N-terminal ubiquitin-like domain (UBL), a tandem Tudor domain (TTD), a plant homeodomain (PHD) domain, a SET and RING finger associated (SRA) domain, and a C-terminal C3HC4-type RING-HC finger. It specifically binds to hemimethylated DNA, double-stranded CpG dinucleotides, and recruits the maintenance methyltransferase DNMT1 to its hemimethylated DNA substrate through its SRA domain. UHRF1-dependent H3K23 ubiquitylation has an essential role in maintenance DNA methylation and replication. The tandem Tudor domain directs UHRF1 binding to the heterochromatin mark histone H3K9me3 and the PHD domain targets UHRF1 to unmodified histone H3 in euchromatic regions. The RING-HC finger exhibits both autocatalytic E3 ubiquitin (Ub) ligase activity and activity against histone H3 and DNMT1.


Pssm-ID: 438425 [Multi-domain]  Cd Length: 84  Bit Score: 135.94  E-value: 7.80e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124430766 720 EGPNFLKKLEQSFMCVCCQELVYQPVTTECFHNVCKDCLQRSFKAQVFSCPACRHDLGQNYVMVLNETLQTLLDLFFPGY 799
Cdd:cd16769    1 PFQLFLSKVEETFQCICCQELVFRPITTVCQHNVCKDCLDRSFRAQVFSCPACRYDLGRSYAMQVNQPLQTVLNQLFPGY 80

                 ....
gi 124430766 800 SKGR 803
Cdd:cd16769   81 GNGR 84
Ubl_UHRF1 cd17122
ubiquitin-like (Ubl) domain found in ubiquitin-like PHD and RING finger domain-containing ...
1-74 7.10e-34

ubiquitin-like (Ubl) domain found in ubiquitin-like PHD and RING finger domain-containing protein 1(UHRF1); UHRF1, also termed inverted CCAAT box-binding protein of 90 kDa, or nuclear protein 95, or nuclear zinc finger protein Np95 (Np95), or RING finger protein 106, or transcription factor ICBP90, or E3 ubiquitin-protein ligase UHRF1, is a unique chromatin effector protein that integrates the recognition of both histone PTMs and DNA methylation. It is essential for cell proliferation and plays a critical role in the development and progression of many human carcinomas, such as laryngeal squamous cell carcinoma, gastric cancer, esophageal squamous cell carcinoma, colorectal cancer, prostate cancer, and breast cancer. UHRF1 can acts as a transcriptional repressor through its binding to histone H3 when it is unmodified at Arg2. Its overexpression in human lung fibroblasts results in downregulation of expression of the tumor suppressor pRB. It also plays a role in transcriptional repression of the cell cycle regulator p21.Moreover, UHRF1-dependent repression of factors can facilitate the G1-S transition. It interacts with Tat-interacting protein of 60 kDa (TIP60) and induces degradation-independent ubiquitination ofTIP60. It is also an N-methylpurine DNA glycosylase (MPG)-interacting protein that binds MPG in a p53status-independent manner in the DNA base excision repair (BER) pathway. In addition, UHRF1 functions as an epigenetic regulator that is important for multiple aspects of epigenetic regulation, including maintenance of DNA methylation patterns and recognition of various histone modifications. UHRF1 contains an N-terminal ubiquitin-like domain (Ubl), a tandem Tudor domain (TTD), a plant homeodomain (PHD) finger, a SET and RING finger associated (SRA) domain, and a C-terminal RING-finger domain. It specifically binds to hemimethylated DNA, double-stranded CpG dinucleotides, and recruits the maintenance methyltransferase DNMT1 to its hemimethylated DNA substrate through its SRA domain. UHRF1-dependent H3K23 ubiquitination has an essential role in maintenance DNA methylation and replication. The tandem Tudor domain directs UHRF1 binding to the heterochromatin mark histone H3K9me3 and the PHD finger targets UHRF1 to unmodified histone H3 in euchromatic regions. The RING-finger domain exhibits both autocatalytic E3 ubiquitin (Ub) ligase activity and activity against histone H3 and DNMT1.


Pssm-ID: 340642  Cd Length: 74  Bit Score: 124.21  E-value: 7.10e-34
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 124430766   1 MWIQVRTIDGSQTRTIEDVSRKATIEELRERVWALFDVRPECQRLFYRGKQLENGYTLFDYDVGLNDIIQLLVR 74
Cdd:cd17122    1 MWIQVRTMDGKETHRIDSLSKLTKVEELRQKIQELFGVEPERQRLFYRGKQMEDGHTLFDYSVGLNDIVQLLVR 74
Tudor_UHRF_rpt2 cd20388
second Tudor domain found in the UHRF (ubiquitin-like PHD and RING finger domain-containing ...
240-312 6.51e-32

second Tudor domain found in the UHRF (ubiquitin-like PHD and RING finger domain-containing protein) family; The UHRF family includes UHRF1 and UHRF2. UHRF1 is a unique chromatin effector protein that integrates the recognition of both histone PTMs and DNA methylation. It is essential for cell proliferation and plays a critical role in the development and progression of many human carcinomas, such as laryngeal squamous cell carcinoma (LSCC), gastric cancer (GC), esophageal squamous cell carcinoma (ESCC), colorectal cancer, prostate cancer, and breast cancer. UHRF1 acts as a transcriptional repressor through its binding to histone H3 when it is unmodified at Arg2. Its overexpression in human lung fibroblasts results in downregulation of expression of the tumour suppressor pRB. It also plays a role in transcriptional repression of the cell cycle regulator p21. It is also an N-methylpurine DNA glycosylase (MPG)-interacting protein that binds MPG in a p53 status-independent manner in the DNA base excision repair (BER) pathway. In addition, UHRF1 functions as an epigenetic regulator that is important for multiple aspects of epigenetic regulation, including maintenance of DNA methylation patterns and recognition of various histone modifications. UHRF2 was originally identified as a ubiquitin ligase acting as a small ubiquitin-like modifier (SUMO) E3 ligase that enhances zinc finger protein 131 (ZNF131) SUMOylation but does not enhance ZNF131 ubiquitination. It also ubiquitinates PCNP, a PEST-containing nuclear protein. Moreover, UHRF2 functions as a nuclear protein involved in cell-cycle regulation and has been implicated in tumorigenesis. It interacts with cyclins, CDKs, p53, pRB, PCNA, HDAC1, DNMTs, G9a, methylated histone H3 lysine 9, and methylated DNA. It interacts with the cyclin E-CDK2 complex, ubiquitinates cyclins D1 and E1, induces G1 arrest, and is involved in the G1/S transition regulation. Both UHRF1 and UHRF2 contain an N-terminal ubiquitin-like domain (UBL), a tandem Tudor domain (TTD), a plant homeodomain(PHD) finger, a SET- and RING-associated (SRA) domain, and a C-terminal RING finger. The model corresponds to the second Tudor domain. The tandem Tudor domain directs binding of UHRF to the heterochromatin mark histone H3K9me3.


Pssm-ID: 410459  Cd Length: 72  Bit Score: 118.51  E-value: 6.51e-32
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 124430766 240 WNELNVGDVVMVNYNVENPGKRGFWYDAEITTLKTIsRTKKEVRVKVFLGGSEGTLNDCRVMSVDEIFKIEKP 312
Cdd:cd20388    1 WDDLKVGQTVMVNYNIDDPKERGYWYDAEITKKRNT-RTKKELTGTLYLGPDLTPLEDCRIKFVDEIFKIEKP 72
RING-HC_UHRF cd16613
RING finger, HC subclass, found in ubiquitin-like PHD and RING finger domain-containing ...
732-777 9.30e-30

RING finger, HC subclass, found in ubiquitin-like PHD and RING finger domain-containing proteins, UHRF1 and UHRF2, and similar proteins; UHRF1 is a unique chromatin effector protein that integrates the recognition of both histone PTMs and DNA methylation. It is essential for cell proliferation and plays a critical role in the development and progression of many human carcinomas, such as laryngeal squamous cell carcinoma (LSCC), gastric cancer (GC), esophageal squamous cell carcinoma (ESCC), colorectal cancer, prostate cancer, and breast cancer. UHRF1 acts as a transcriptional repressor through its binding to histone H3 when it is unmodified at Arg2. Its overexpression in human lung fibroblasts results in downregulation of expression of the tumor suppressor pRB. It also plays a role in transcriptional repression of the cell cycle regulator p21. Moreover, UHRF1-dependent repression of transcription factors can facilitate the G1-S transition. It interacts with Tat-interacting protein of 60 kDa (TIP60) and induces degradation-independent ubiquitination of TIP60. It is also an N-methylpurine DNA glycosylase (MPG)-interacting protein that binds MPG in a p53 status-independent manner in the DNA base excision repair (BER) pathway. In addition, UHRF1 functions as an epigenetic regulator that is important for multiple aspects of epigenetic regulation, including maintenance of DNA methylation patterns and recognition of various histone modifications. UHRF2 was originally identified as a ubiquitin ligase acting as a small ubiquitin-like modifier (SUMO) E3 ligase that enhances zinc finger protein 131 (ZNF131) SUMOylation, but does not enhance ZNF131 ubiquitination. It also ubiquitinates PCNP, a PEST-containing nuclear protein. Moreover, UHRF2 functions as a nuclear protein involved in cell-cycle regulation and has been implicated in tumorigenesis. It interacts with cyclins, CDKs, p53, pRB, PCNA, HDAC1, DNMTs, G9a, methylated histone H3 lysine 9, and methylated DNA. It interacts with the cyclin E-CDK2 complex, ubiquitinates cyclins D1 and E1, induces G1 arrest, and is involved in the G1/S transition regulation. Furthermore, UHRF2 is a direct transcriptional target of the transcription factor E2F-1 in the induction of apoptosis. It recruits HDAC1 and binds to methyl-CpG. UHRF2 also participates in the maturation of Hepatitis B virus (HBV) by interacting with the HBV core protein and promoting its degradation. Both UHRF1 and UHRF2 contain an N-terminal ubiquitin-like domain (UBL), a tandem Tudor domain (TTD), a plant homeodomain (PHD) finger, a SET- and RING-associated (SRA) domain, and a C-terminal C3HC4-type RING-HC finger.


Pssm-ID: 438275 [Multi-domain]  Cd Length: 46  Bit Score: 111.29  E-value: 9.30e-30
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 124430766 732 FMCVCCQELVYQPVTTECFHNVCKDCLQRSFKAQVFSCPACRHDLG 777
Cdd:cd16613    1 FTCICCQELVYKPITTPCKHNICKSCLQRSFKAEVYTCPACRHDLG 46
PHD_UHRF2 cd15617
PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein 2 (UHRF2); ...
347-393 3.87e-28

PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein 2 (UHRF2); UHRF2 (also termed Np95/ICBP90-like RING finger protein (NIRF), Np95-like RING finger protein, nuclear protein 97, nuclear zinc finger protein Np97, RING finger protein 107, or E3 ubiquitin-protein ligase UHRF2) was originally identified as a ubiquitin ligase acting as a small ubiquitin-like modifier (SUMO) E3 ligase that enhances zinc finger protein 131 (ZNF131) SUMOylation but does not enhance ZNF131 ubiquitination. It also ubiquitinates PCNP, a PEST-containing nuclear protein. Moreover, UHRF2 functions as a nuclear protein involved in cell-cycle regulation and has been implicated in tumorigenesis. It interacts with cyclins, CDKs,p53, pRB, PCNA, HDAC1, DNMTs, G9a, methylated histone H3 lysine 9, and methylated DNA. It interacts with the cyclin E-CDK2 complex, ubiquitinates cyclins D1 and E1, induces G1 arrest, and is involved in the G1/S transition regulation. Furthermore, UHRF2 is a direct transcriptional target of the transcription factor E2F-1 in the induction of apoptosis. It recruits HDAC1 and binds to methyl-CpG. UHRF2 also participates in the maturation of Hepatitis B virus (HBV) by interacting with the HBV core protein and promoting its degradation. UHRF2 contains an N-terminal ubiquitin-like domain (UBL), a tandem Tudor domain (TTD), a plant homeodomain (PHD) finger, a SET- and RING-associated (SRA) domain, and a C-terminal RING finger.


Pssm-ID: 277089  Cd Length: 47  Bit Score: 106.96  E-value: 3.87e-28
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 124430766 347 SCHKCGEKRDPNMQLLCDECNMAYHIYCLSPPLDKVPEEEYWYCPSC 393
Cdd:cd15617    1 SCYVCGGKQDAHMQLLCDECNMAYHIYCLNPPLDKIPEDEDWYCPSC 47
PHD_UHRF1_2 cd15525
PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein UHRF1 and ...
347-393 2.52e-27

PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein UHRF1 and UHRF2; UHRF1 is a unique chromatin effector protein that integrates the recognition of both histone PTMs and DNA methylation. It is essential for cell proliferation and plays a critical role in the development and progression of many human carcinomas, such as laryngeal squamous cell carcinoma (LSCC), gastric cancer (GC), esophageal squamous cell carcinoma (ESCC), colorectal cancer, prostate cancer, and breast cancer. UHRF1 acts as a transcriptional repressor through its binding to histone H3 when it is unmodified at Arg2. Its overexpression in human lung fibroblasts results in downregulation of expression of the tumour suppressor pRB. It also plays a role in transcriptional repression of the cell cycle regulator p21. Moreover, UHRF1-dependent repression of transcription factors can facilitate the G1-S transition. It interacts with Tat-interacting protein of 60 kDa (TIP60) and induces degradation-independent ubiquitination of TIP60. It is also an N-methylpurine DNA glycosylase (MPG)-interacting protein that binds MPG in a p53 status-independent manner in the DNA base excision repair (BER) pathway. In addition, UHRF1 functions as an epigenetic regulator that is important for multiple aspects of epigenetic regulation, including maintenance of DNA methylation patterns and recognition of various histone modifications. UHRF2 was originally identified as a ubiquitin ligase acting as a small ubiquitin-like modifier (SUMO) E3 ligase that enhances zinc finger protein 131 (ZNF131) SUMOylation but does not enhance ZNF131 ubiquitination. It also ubiquitinates PCNP, a PEST-containing nuclear protein. Moreover, UHRF2 functions as a nuclear protein involved in cell-cycle regulation and has been implicated in tumorigenesis. It interacts with cyclins, CDKs, p53, pRB, PCNA, HDAC1, DNMTs, G9a, methylated histone H3 lysine 9, and methylated DNA. It interacts with the cyclin E-CDK2 complex, ubiquitinates cyclins D1 and E1, induces G1 arrest, and is involved in the G1/S transition regulation. Furthermore, UHRF2 is a direct transcriptional target of the transcription factor E2F-1 in the induction of apoptosis. It recruits HDAC1 and binds to methyl-CpG. UHRF2 also participates in the maturation of Hepatitis B virus (HBV) by interacting with the HBV core protein and promoting its degradation. Both UHRF1 and UHRF2 contain an N-terminal ubiquitin-like domain (UBL), a tandem Tudor domain (TTD), a plant homeodomain (PHD) finger, a SET- and RING-associated (SRA) domain, and a C-terminal RING finger.


Pssm-ID: 277000  Cd Length: 47  Bit Score: 104.37  E-value: 2.52e-27
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 124430766 347 SCHKCGEKRDPNMQLLCDECNMAYHIYCLSPPLDKVPEEEYWYCPSC 393
Cdd:cd15525    1 ACHVCGGKQDPEKQLLCDECDMAYHLYCLDPPLTSLPDDDEWYCPDC 47
Tudor_UHRF1_rpt2 cd20457
second Tudor domain found in ubiquitin-like PHD and RING finger domain-containing protein 1 ...
240-312 4.23e-26

second Tudor domain found in ubiquitin-like PHD and RING finger domain-containing protein 1 (UHRF1) and similar proteins; UHRF1, also called inverted CCAAT box-binding protein of 90 kDa, nuclear protein 95, nuclear zinc finger protein Np95 (Np95), RING finger protein 106, transcription factor ICBP90, or E3 ubiquitin-protein ligase UHRF1, is a unique chromatin effector protein that integrates the recognition of both histone PTMs and DNA methylation. It is essential for cell proliferation and plays a critical role in the development and progression of many human carcinomas, such as laryngeal squamous cell carcinoma (LSCC), gastric cancer (GC), esophageal squamous cell carcinoma (ESCC), colorectal cancer, prostate cancer, and breast cancer. UHRF1 can act as a transcriptional repressor through its binding to histone H3 when it is unmodified at Arg2. Its overexpression in human lung fibroblasts results in downregulation of expression of the tumour suppressor pRB. It also plays a role in transcriptional repression of the cell cycle regulator p21. Moreover, UHRF1-dependent repression of factors can facilitate the G1-S transition. It interacts with Tat-interacting protein of 60 kDa (TIP60) and induces degradation-independent ubiquitination of TIP60. It is also a N-methylpurine DNA glycosylase (MPG)-interacting protein that binds MPG in a p53 status-independent manner in the DNA base excision repair (BER) pathway. In addition, UHRF1 functions as an epigenetic regulator that is important for multiple aspects of epigenetic regulation, including maintenance of DNA methylation patterns and recognition of various histone modifications. UHRF1 contains an N-terminal ubiquitin-like domain (UBL), a tandem Tudor domain (TTD), a plant homeodomain (PHD) domain, a SET- and RING- associated (SRA) domain, and a C-terminal RING-finger domain. It specifically binds to hemimethylated DNA, double-stranded CpG dinucleotides, and recruits the maintenance methyltransferase DNMT1 to its hemimethylated DNA substrate through its SRA domain. UHRF1-dependent H3K23 ubiquitylation has an essential role in maintenance DNA methylation and replication. The tandem Tudor domain directs UHRF1 binding to the heterochromatin mark histone H3K9me3 and the PHD domain targets UHRF1 to unmodified histone H3 in euchromatic regions. The RING-finger domain exhibit both autocatalytic E3 ubiquitin (Ub) ligase activity and activity against histone H3 and DNMT1. The model corresponds to the second Tudor domain.


Pssm-ID: 410528  Cd Length: 72  Bit Score: 101.82  E-value: 4.23e-26
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 124430766 240 WNELNVGDVVMVNYNVENPGKRGFWYDAEITTlKTISRTKKEVRVKVFLGGSEGTLNDCRVMSVDEIFKIEKP 312
Cdd:cd20457    1 WQDLEVGQVVMVNYNPDNPKERGFWYDAEISR-KRETRTARELYANVVLGDAGDSLNDCRIIFVDEIYKIERP 72
Tudor_UHRF1_rpt1 cd20455
first Tudor domain found in ubiquitin-like PHD and RING finger domain-containing protein 1 ...
127-238 4.42e-26

first Tudor domain found in ubiquitin-like PHD and RING finger domain-containing protein 1 (UHRF1) and similar proteins; UHRF1, also called inverted CCAAT box-binding protein of 90 kDa, nuclear protein 95, nuclear zinc finger protein Np95 (Np95), RING finger protein 106, transcription factor ICBP90, or E3 ubiquitin-protein ligase UHRF1, is a unique chromatin effector protein that integrates the recognition of both histone PTMs and DNA methylation. It is essential for cell proliferation and plays a critical role in the development and progression of many human carcinomas, such as laryngeal squamous cell carcinoma (LSCC), gastric cancer (GC), esophageal squamous cell carcinoma (ESCC), colorectal cancer, prostate cancer, and breast cancer. UHRF1 can act as a transcriptional repressor through its binding to histone H3 when it is unmodified at Arg2. Its overexpression in human lung fibroblasts results in downregulation of expression of the tumour suppressor pRB. It also plays a role in transcriptional repression of the cell cycle regulator p21. Moreover, UHRF1-dependent repression of factors can facilitate the G1-S transition. It interacts with Tat-interacting protein of 60 kDa (TIP60) and induces degradation-independent ubiquitination of TIP60. It is also a N-methylpurine DNA glycosylase (MPG)-interacting protein that binds MPG in a p53 status-independent manner in the DNA base excision repair (BER) pathway. In addition, UHRF1 functions as an epigenetic regulator that is important for multiple aspects of epigenetic regulation, including maintenance of DNA methylation patterns and recognition of various histone modifications. UHRF1 contains an N-terminal ubiquitin-like domain (UBL), a tandem Tudor domain (TTD), a plant homeodomain (PHD) domain, a SET- and RING- associated (SRA) domain, and a C-terminal RING-finger domain. It specifically binds to hemimethylated DNA, double-stranded CpG dinucleotides, and recruits the maintenance methyltransferase DNMT1 to its hemimethylated DNA substrate through its SRA domain. UHRF1-dependent H3K23 ubiquitylation has an essential role in maintenance DNA methylation and replication. The tandem Tudor domain directs UHRF1 binding to the heterochromatin mark histone H3K9me3 and the PHD domain targets UHRF1 to unmodified histone H3 in euchromatic regions. The RING-finger domain exhibit both autocatalytic E3 ubiquitin (Ub) ligase activity and activity against histone H3 and DNMT1. The model corresponds to the first Tudor domain.


Pssm-ID: 410526  Cd Length: 79  Bit Score: 101.89  E-value: 4.42e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124430766 127 LYKVNELVDARDVGLGAWFEAHIHSVTRasdghsrgktplkngssykrtngnvnhnsKENTNKldnvPSTSNSDSVAADE 206
Cdd:cd20455    1 LYKVNEYVDARDTNMGAWFEAQVVRVTR-----------------------------KAPSRD----EPCSSTSRPALEE 47
                         90       100       110
                 ....*....|....*....|....*....|..
gi 124430766 207 DVIYHIEYDEYPESGILEMNVKDLRPRARTIL 238
Cdd:cd20455   48 DVIYHVKYDDYPENGVVQLNSRDVRARARTII 79
Tudor_UHRF_rpt1 cd20387
first Tudor domain found in the UHRF (ubiquitin-like PHD and RING finger domain-containing ...
127-238 4.82e-23

first Tudor domain found in the UHRF (ubiquitin-like PHD and RING finger domain-containing protein) family; The UHRF family includes UHRF1 and UHRF2. UHRF1 is a unique chromatin effector protein that integrates the recognition of both histone PTMs and DNA methylation. It is essential for cell proliferation and plays a critical role in the development and progression of many human carcinomas, such as laryngeal squamous cell carcinoma (LSCC), gastric cancer (GC), esophageal squamous cell carcinoma (ESCC), colorectal cancer, prostate cancer, and breast cancer. UHRF1 acts as a transcriptional repressor through its binding to histone H3 when it is unmodified at Arg2. Its overexpression in human lung fibroblasts results in downregulation of expression of the tumour suppressor pRB. It also plays a role in transcriptional repression of the cell cycle regulator p21. It is also an N-methylpurine DNA glycosylase (MPG)-interacting protein that binds MPG in a p53 status-independent manner in the DNA base excision repair (BER) pathway. In addition, UHRF1 functions as an epigenetic regulator that is important for multiple aspects of epigenetic regulation, including maintenance of DNA methylation patterns and recognition of various histone modifications. UHRF2 was originally identified as a ubiquitin ligase acting as a small ubiquitin-like modifier (SUMO) E3 ligase that enhances zinc finger protein 131 (ZNF131) SUMOylation but does not enhance ZNF131 ubiquitination. It also ubiquitinates PCNP, a PEST-containing nuclear protein. Moreover, UHRF2 functions as a nuclear protein involved in cell-cycle regulation and has been implicated in tumorigenesis. It interacts with cyclins, CDKs, p53, pRB, PCNA, HDAC1, DNMTs, G9a, methylated histone H3 lysine 9, and methylated DNA. It interacts with the cyclin E-CDK2 complex, ubiquitinates cyclins D1 and E1, induces G1 arrest, and is involved in the G1/S transition regulation. Both UHRF1 and UHRF2 contain an N-terminal ubiquitin-like domain (UBL), a tandem Tudor domain (TTD), a plant homeodomain(PHD) finger, a SET- and RING-associated (SRA) domain, and a C-terminal RING finger. The model corresponds to the first Tudor domain. The tandem Tudor domain directs binding of UHRF to the heterochromatin mark histone H3K9me3.


Pssm-ID: 410458  Cd Length: 73  Bit Score: 93.14  E-value: 4.82e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124430766 127 LYKVNELVDARDVGLGAWFEAHIHSVTRASDGhsrgktplkngssykrtngnvnhnskentnkldnvpstsNSDSVAADE 206
Cdd:cd20387    1 YYKVGDLVDARDPTMGAWFEAKIVRITKKEPN---------------------------------------TNNKTADED 41
                         90       100       110
                 ....*....|....*....|....*....|..
gi 124430766 207 DVIYHIEYDEYPESGILEMNVKDLRPRARTIL 238
Cdd:cd20387   42 DLIYHVKFDDYEEEGPLEVSFKDIRPRARHLI 73
PHD_UHRF1 cd15616
PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein 1 (UHRF1); ...
347-393 5.66e-22

PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein 1 (UHRF1); UHRF1 (also termed inverted CCAAT box-binding protein of 90 kDa, nuclear protein 95, nuclear zinc finger protein Np95 (Np95), RING finger protein 106, transcription factor ICBP90, or E3 ubiquitin-protein ligase UHRF1) is a unique chromatin effector protein that integrates the recognition of both histone PTMs and DNA methylation. It is essential for cell proliferation and plays a critical role in the development and progression of many human carcinomas, such as laryngeal squamous cell carcinoma (LSCC), gastric cancer (GC), esophageal squamous cell carcinoma (ESCC), colorectal cancer, prostate cancer, and breast cancer. UHRF1 acts as a transcriptional repressor through its binding to histone H3 when it is unmodified at Arg2. Its overexpression in human lung fibroblasts results in downregulation of expression of the tumour suppressor pRB. It also plays a role in transcriptional repression of the cell cycle regulator p21. Moreover, UHRF1-dependent repression of transcription factors can facilitate the G1-S transition. It interacts with Tat-interacting protein of 60 kDa (TIP60) and induces degradation-independent ubiquitination of TIP60. It is also an N-methylpurine DNA glycosylase (MPG)-interacting protein that binds MPG in a p53 status-independent manner in the DNA base excision repair (BER) pathway. In addition, UHRF1 functions as an epigenetic regulator that is important for multiple aspects of epigenetic regulation, including maintenance of DNA methylation patterns and recognition of various histone modifications. UHRF1 contains an N-terminal ubiquitin-like domain (UBL), a tandem Tudor domain (TTD), a plant homeodomain (PHD) finger, a SET and RING finger associated (SRA) domain, and a C-terminal RING-finger domain. It specifically binds to hemimethylated DNA, double-stranded CpG dinucleotides, and recruits the maintenance methyltransferase DNMT1 to its hemimethylated DNA substrate through its SRA domain. UHRF1-dependent H3K23 ubiquitylation has an essential role in maintaining DNA methylation and replication. The tandem Tudor domain directs UHRF1 binding to the heterochromatin mark histone H3K9me3 and the PHD finger targets UHRF1 to unmodified histone H3 in euchromatic regions. The RING-finger domain exhibit both autocatalytic E3 ubiquitin (Ub) ligase activity and activity against histone H3 and DNMT1.


Pssm-ID: 277088  Cd Length: 47  Bit Score: 89.26  E-value: 5.66e-22
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 124430766 347 SCHKCGEKRDPNMQLLCDECNMAYHIYCLSPPLDKVPEEEYWYCPSC 393
Cdd:cd15616    1 ACHVCGGKQDPDKQLMCDECDMAFHIYCLNPPLSSIPDDEDWYCPEC 47
PHD_RSF1 cd15543
PHD finger found in Remodeling and spacing factor 1 (Rsf-1); Rsf-1, also termed HBV ...
348-393 1.80e-16

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: 73.46  E-value: 1.80e-16
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 124430766 348 CHKCGEKRDPNMQLLCDECNMAYHIYCLSPPLDKVPEEEyWYCPSC 393
Cdd:cd15543    2 CRKCGLSDHPEWILLCDRCDAGYHTACLRPPLMIIPDGN-WFCPPC 46
PHD_BAZ1A cd15627
PHD finger found in bromodomain adjacent to zinc finger domain protein 1A (BAZ1A); BAZ1A, also ...
348-393 3.57e-14

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: 67.03  E-value: 3.57e-14
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 124430766 348 CHKCGEKRDPNMQLLCDECNMAYHIYCLSPPLDKVPEEEyWYCPSC 393
Cdd:cd15627    2 CRICRRKGDAEKMLLCDGCDRGHHMYCLRPPLKKVPEGD-WFCPDC 46
ubiquitin pfam00240
Ubiquitin family; This family contains a number of ubiquitin-like proteins: SUMO (smt3 homolog) ...
3-76 3.83e-14

Ubiquitin family; This family contains a number of ubiquitin-like proteins: SUMO (smt3 homolog), Nedd8, Elongin B, Rub1, and Parkin. A number of them are thought to carry a distinctive five-residue motif termed the proteasome-interacting motif (PIM), which may have a biologically significant role in protein delivery to proteasomes and recruitment of proteasomes to transcription sites.


Pssm-ID: 425549 [Multi-domain]  Cd Length: 72  Bit Score: 67.97  E-value: 3.83e-14
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 124430766    3 IQVRTIDGSQTrTIEdVSRKATIEELRERVWALFDVRPECQRLFYRGKQLENGYTLFDYDVGLNDIIQLLVRPD 76
Cdd:pfam00240   1 ITVKTLDGKKI-TLE-VDPTDTVLELKEKIAEKEGVPPEQQRLIYSGKVLEDDQTLGEYGIEDGSTIHLVLRQR 72
Ubl_ubiquitin_like cd17039
ubiquitin-like (Ubl) domain found in ubiquitin and ubiquitin-like Ubl proteins; Ubiquitin-like ...
3-72 1.25e-13

ubiquitin-like (Ubl) domain found in ubiquitin and ubiquitin-like Ubl proteins; Ubiquitin-like (Ubl) proteins have a similar ubiquitin (Ub) beta-grasp fold and attach to other proteins in a Ubl manner but with biochemically distinct roles. Ub and Ubl proteins conjugate and deconjugate via ligases and peptidases to covalently modify target polypeptides. Some Ubl domains have adaptor roles in Ub-signaling by mediating protein-protein interaction. Prokaryotic sulfur carrier proteins are Ub-related proteins that can be activated in an ATP-dependent manner. Polyubiquitination signals for a diverse set of cellular events via different isopeptide linkages formed between the C terminus of one ubiquitin (Ub) and the epsilon-amine of K6, K11, K27, K29, K33, K48, or K63 of a second Ub. One of these seven lysine residues (K27, Ub numbering) is conserved in this Ubl_ubiquitin_like family. K27-linked Ub chains are versatile and can be recognized by several downstream receptor proteins. K27 has roles beyond chain linkage, such as in Ubl NEDD8 (which contains many of the same lysines (K6, K11, K27, K33, K48) as Ub) where K27 has a role (other than conjugation) in the mechanism of protein neddylation.


Pssm-ID: 340559 [Multi-domain]  Cd Length: 68  Bit Score: 66.08  E-value: 1.25e-13
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124430766   3 IQVRTIDGsQTRTIEdVSRKATIEELRERVWALFDVRPECQRLFYRGKQLENGYTLFDYDVGLNDIIQLL 72
Cdd:cd17039    1 ITVKTLDG-KTYTVE-VDPDDTVADLKEKIEEKTGIPVEQQRLIYNGKELKDDKTLSDYGIKDGSTIHLV 68
PHD1_Lid2p_like cd15519
PHD finger 1 found in Schizosaccharomyces pombe Lid2 complex component Lid2p and similar ...
348-393 1.36e-13

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: 65.56  E-value: 1.36e-13
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 124430766 348 CHKCGEKRDPNMQLLCDECNMAYHIYCLSPPLDKVPEEEyWYCPSC 393
Cdd:cd15519    2 CEVCGLDDNEGEVLLCDGCDAEYHTSCLDPPLGEIPPGT-WFCPSC 46
PHD_BAZ1A_like cd15544
PHD finger found in bromodomain adjacent to zinc finger domain protein BAZ1A and BAZ1B; BAZ1A, ...
348-393 1.36e-12

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: 62.43  E-value: 1.36e-12
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 124430766 348 CHKCGEKRDPNMQLLCDECNMAYHIYCLSPPLDKVPEEEyWYCPSC 393
Cdd:cd15544    2 CKVCRKKGDPDNMILCDGCDKAFHLYCLRPALREVPSGD-WFCPAC 46
PHD5_KMT2C_like cd15513
PHD finger 5 found in Histone-lysine N-methyltransferase 2C (KMT2C) and PHD finger 4 found in ...
348-393 3.02e-12

PHD finger 5 found in Histone-lysine N-methyltransferase 2C (KMT2C) and PHD finger 4 found in KMT2D; KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3), or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named MLL4, a fourth human homolog of Drosophila trithorax, located on chromosome 12. It enzymatically generates trimethylated histone H3 Lysine 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. KMT2D is also a part of ASCOM. Both KMT2C and KMT2D contain the catalytic domain SET, several plant homeodomain (PHD) fingers, extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions. This model corresponds to the fifth PHD finger of KMT2C and the fourth PHD finger of KMT2D.


Pssm-ID: 276988  Cd Length: 47  Bit Score: 61.72  E-value: 3.02e-12
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 124430766 348 CHKCGEKRDPNMQLLCDECNMAYHIYCLSPPLDKVPEEEyWYCPSC 393
Cdd:cd15513    2 CEGCGKASDESRLLLCDDCDISYHTYCLDPPLQTVPKGG-WKCKWC 46
PHD_PHRF1 cd15536
PHD finger found in PHD and RING finger domain-containing protein 1 (PHRF1); PHRF1, also ...
348-393 9.12e-12

PHD finger found in PHD and RING finger domain-containing protein 1 (PHRF1); PHRF1, also termed KIAA1542, or CTD-binding SR-like protein rA9, is a ubiquitin ligase that induces the ubiquitination of TGIF (TG-interacting factor) at lysine 130. It acts as a tumor suppressor that promotes the transforming growth factor (TGF)-beta cytostatic program through selective release of TGIF-driven promyelocytic leukemia protein (PML) inactivation. PHRF1 contains a plant homeodomain (PHD) finger and a RING finger.


Pssm-ID: 277011  Cd Length: 46  Bit Score: 60.12  E-value: 9.12e-12
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 124430766 348 CHKCGEKRDPNMQLLCDECNMAYHIYCLSPPLDKVPEEEyWYCPSC 393
Cdd:cd15536    2 CEVCGRSDREDRLLLCDGCDAGYHMECLTPPLDEVPIEE-WFCPEC 46
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
348-393 4.51e-11

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: 58.38  E-value: 4.51e-11
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 124430766   348 CHKCGEKRDPNMQLLCDECNMAYHIYCLSPPLDKVPEEEYWYCPSC 393
Cdd:smart00249   2 CSVCGKPDDGGELLQCDGCDRWYHQTCLGPPLLEEEPDGKWYCPKC 47
PHD pfam00628
PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...
348-394 5.13e-11

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: 58.27  E-value: 5.13e-11
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 124430766  348 CHKCGEKRDPNMQLLCDECNMAYHIYCLSPPLDKVPE-EEYWYCPSCK 394
Cdd:pfam00628   2 CAVCGKSDDGGELVQCDGCDDWFHLACLGPPLDPAEIpSGEWLCPECK 49
PHD_PRHA_like cd15504
PHD finger found in Arabidopsis thaliana pathogenesis-related homeodomain protein (PRHA) and ...
346-393 7.83e-11

PHD finger found in Arabidopsis thaliana pathogenesis-related homeodomain protein (PRHA) and similar proteins; PRHA is a homeodomain protein encoded by a single-copy Arabidopsis thaliana homeobox gene, prha. It shows the capacity to bind to TAATTG core sequence elements but requires additional adjacent bases for high-affinity binding. PRHA contains a plant homeodomain (PHD) finger, a homeodomain, peptide repeats and a putative leucine zipper dimerization domain.


Pssm-ID: 276979  Cd Length: 53  Bit Score: 57.83  E-value: 7.83e-11
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 124430766 346 CSCHKCGEKRDPNMQLLCD-ECNMAYHIYCLSPPL---DKVPEEEYWYCPSC 393
Cdd:cd15504    2 CAKCQSGEASPDNDILLCDgGCNRAYHQKCLEPPLlteDIPPEDEGWLCPLC 53
PHD1_KDM5A_like cd15515
PHD finger 1 found in Lysine-specific demethylase KDM5A, KDM5B, KDM5C, KDM5D and similar ...
348-393 1.58e-10

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: 56.63  E-value: 1.58e-10
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 124430766 348 CHKCGEKRDPNMQLLCDECNMAYHIYCLSPPLDKVPEEEyWYCPSC 393
Cdd:cd15515    2 CQVCGRGDDEDKLLLCDGCDDSYHTFCLIPPLPDIPPGD-WRCPKC 46
PHD_BAZ1B cd15628
PHD finger found in bromodomain adjacent to zinc finger domain protein 1B (BAZ1B); BAZ1B, also ...
348-393 2.15e-10

PHD finger found in bromodomain adjacent to zinc finger domain protein 1B (BAZ1B); 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. BAZ1B 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: 277098  Cd Length: 46  Bit Score: 56.29  E-value: 2.15e-10
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 124430766 348 CHKCGEKRDPNMQLLCDECNMAYHIYCLSPPLDKVPEEEyWYCPSC 393
Cdd:cd15628    2 CKVCRKKGEDDKLILCDECNQAFHLFCLRPALYEVPDGE-WMCPAC 46
PHD1_Lid_like cd15605
PHD finger 1 found in Drosophila melanogaster protein little imaginal discs (Lid) and similar ...
348-393 2.78e-10

PHD finger 1 found in Drosophila melanogaster protein little imaginal discs (Lid) and similar proteins; Drosophila melanogaster Lid, also termed Retinoblastoma-binding protein 2 homolog, is identified genetically as a trithorax group (trxG) protein that is a Drosophila homolog of the human protein JARID1A/kdm5A, a member of the JARID subfamily within the JmjC proteins. Lid 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. Lid 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 first PHD finger of Lid.


Pssm-ID: 277078  Cd Length: 46  Bit Score: 55.92  E-value: 2.78e-10
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 124430766 348 CHKCGEKRDPNMQLLCDECNMAYHIYCLSPPLDKVPEEEyWYCPSC 393
Cdd:cd15605    2 CHTCGRGDGEESMLLCDGCDDSYHTFCLLPPLSEVPKGD-WRCPKC 46
PHD2_CHD_II cd15532
PHD finger 2 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins; Class II CHD ...
347-393 5.04e-10

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: 55.36  E-value: 5.04e-10
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 124430766 347 SCHKCGekrDPNMQLLCDECNMAYHIYCLSPPLDKVPEEEyWYCPSC 393
Cdd:cd15532    1 FCRVCK---DGGELLCCDGCPSSYHLHCLNPPLAEIPDGD-WFCPRC 43
UBQ smart00213
Ubiquitin homologues; Ubiquitin-mediated proteolysis is involved in the regulated turnover of ...
3-74 9.68e-10

Ubiquitin homologues; Ubiquitin-mediated proteolysis is involved in the regulated turnover of proteins required for controlling cell cycle progression


Pssm-ID: 214563 [Multi-domain]  Cd Length: 72  Bit Score: 55.34  E-value: 9.68e-10
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 124430766     3 IQVRTIDGSqTRTIEdVSRKATIEELRERVWALFDVRPECQRLFYRGKQLENGYTLFDYDVGLNDIIQLLVR 74
Cdd:smart00213   3 LTVKTLDGK-TITLE-VKPSDTVSELKEKIAELTGIPPEQQRLIYKGKVLEDDRTLADYGIQDGSTIHLVLR 72
PHD_BAZ2A_like cd15545
PHD finger found in bromodomain adjacent to zinc finger domain protein 2A (BAZ2A) and 2B ...
347-393 1.22e-09

PHD finger found in bromodomain adjacent to zinc finger domain protein 2A (BAZ2A) and 2B (BAZ2B); BAZ2A, also termed transcription termination factor I-interacting protein 5 (TTF-I-interacting protein 5, or Tip5), or WALp3, is an epigenetic regulator. It has been implicated in epigenetic rRNA gene silencing, as the large subunit of the SNF2h-containing chromatin-remodeling complex NoRC that induces nucleosome sliding in an ATP- and histone H4 tail-dependent fashion. BAZ2A has also been shown to be broadly overexpressed in prostate cancer, to regulate numerous protein-coding genes and to cooperate with EZH2 (enhancer of zeste homolog 2) to maintain epigenetic silencing at genes repressed in prostate cancer metastasis. Its overexpression is tightly associated with a prostate cancer subtype displaying CpG island methylator phenotype (CIMP) in tumors and with prostate cancer recurrence in patients. BAZ2B, also termed WALp4, is a bromodomain-containing protein whose biological role is still elusive. It shows high sequence similarly with BAZ2A. Both BAZ2A and BAZ2B contain a TAM (TIP5/ARBP/MBD) domain, a DDT domain, four AT-hooks, BAZ 1 and BAZ 2 motifs, a WAKZ (WSTF/Acf1/KIAA0314/ZK783.4) motif, a plant homeodomain (PHD) finger, and a bromodomain. BAZ2B also harbors an extra Apolipophorin-III like domain in its N-terminal region.


Pssm-ID: 277020  Cd Length: 46  Bit Score: 54.24  E-value: 1.22e-09
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 124430766 347 SCHKCGEKRDPNMQLLCDECNMAYHIYCLSPPLDKVPEEEyWYCPSC 393
Cdd:cd15545    1 SCQICRSGDNEDQLLLCDGCDRGYHTYCFKPKMTNVPEGD-WFCPEC 46
RING-HC cd16449
HC subclass of RING (RING-HC) finger and its variants; The RING finger is a specialized type ...
732-772 1.52e-09

HC subclass of RING (RING-HC) finger and its variants; The RING finger is a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc. It is defined by the "cross-brace" motif that chelates zinc atoms by eight amino acid residues, typically Cys or His, arranged in a characteristic spacing. Canonical RING motifs have been categorized into two major subclasses, RING-HC (C3HC4-type) and RING-H2 (C3H2C3-type), according to their Cys/His content. There are also many variants of RING fingers. Some have a different Cys/His pattern. Some lack a single Cys or His residue at typical Zn ligand positions, especially, the fourth or eighth zinc ligand is prevalently exchanged for an Asp, which can chelate Zn in a RING finger as well. This family corresponds to the HC subclass of RING (RING-HC) fingers that are characterized by containing C3HC4-type canonical RING-HC fingers or noncanonical RING-HC finger variants, including C4C4-, C3HC3D-, C2H2C4-, and C3HC5-type modified RING-HC fingers. The canonical RING-HC finger has been defined as C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C. It binds two Zn ions in a unique "cross-brace" arrangement, which distinguishes it from tandem zinc fingers and other similar motifs. RING-HC fingers can be found in a group of diverse proteins with a variety of cellular functions, including oncogenesis, development, viral replication, signal transduction, the cell cycle, and apoptosis. Many of them are ubiquitin-protein ligases (E3s) that serve as scaffolds for binding to ubiquitin-conjugating enzymes (E2s, also referred to as ubiquitin carrier proteins or UBCs) in close proximity to substrate proteins, which enables efficient transfer of ubiquitin from E2 to the substrates.


Pssm-ID: 438113 [Multi-domain]  Cd Length: 41  Bit Score: 53.64  E-value: 1.52e-09
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 124430766 732 FMCVCCQELVYQPVTTECFHNVCKDCLQRSFKAQVFSCPAC 772
Cdd:cd16449    1 LECPICLERLKDPVLLPCGHVFCRECIRRLLESGSIKCPIC 41
RING-HC_TRIM25_C-IV cd16597
RING finger, HC subclass, found in tripartite motif-containing protein TRIM25 and similar ...
728-773 2.94e-09

RING finger, HC subclass, found in tripartite motif-containing protein TRIM25 and similar proteins; TRIM25, also known as estrogen-responsive finger protein (EFP), RING finger protein 147 (RNF147), or RING-type E3 ubiquitin transferase, is an E3 ubiquitin/ISG15 ligase that is induced by estrogen and is therefore particularly abundant in placenta and uterus. TRIM25 regulates various cellular processes through E3 ubiquitin ligase activity, transferring ubiquitin and ISG15 to target proteins. It mediates K63-linked polyubiquitination of retinoic acid inducible gene I (RIG-I) that is crucial for downstream antiviral interferon signaling. It is also required for melanoma differentiation-associated gene 5 (MDA5) and mitochondrial antiviral signaling (MAVS, also known as IPS-1, VISA, Cardiff) mediated activation of nuclear factor-kappaB (NF-kappaB) and interferon production. Upon UV irradiation, TRIM25 interacts with mono-ubiquitinated PCNA and promotes its ISG15 modification (ISGylation), suggesting a crucial role in termination of error-prone translesion DNA synthesis. TRIM25 also functions as a novel regulator of p53 and Mdm2. It enhances p53 and Mdm2 abundance by inhibiting their ubiquitination and degradation in 26S proteasomes. Meanwhile, it inhibits p53's transcriptional activity and dampens the response to DNA damage, and is essential for medaka development and this dependence is rescued by silencing of p53. Moreover, TRIM25 is involved in the host cellular innate immune response against retroviral infection. It interferes with the late stage of feline leukemia virus (FeLV) replication. Furthermore, TRIM25 acts as an oncogene in gastric cancer. Its blockade by RNA interference inhibits migration and invasion of gastric cancer cells through transforming growth factor-beta (TGF-beta) signaling, suggesting it presents a novel target for the detection and treatment of gastric cancer. In addition, TRIM25 acts as an RNA-specific activator for Lin28a/TuT4-mediated uridylation. TRIM25 belongs to the C-IV subclass of TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain.


Pssm-ID: 438259 [Multi-domain]  Cd Length: 71  Bit Score: 53.85  E-value: 2.94e-09
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                 ....*....|....*....|....*....|....*....|....*....
gi 124430766 728 LEQSFMCVCCQELVYQPVTTECFHNVCKDCLQRSFKAQ---VFSCPACR 773
Cdd:cd16597    2 LEEELTCSICLELFKDPVTLPCGHNFCGVCIEKTWDSQhgsEYSCPQCR 50
RING-HC_ScPSH1-like cd16568
RING finger, HC subclass, found in Saccharomyces cerevisiae POB3/SPT16 histone-associated ...
728-779 3.26e-09

RING finger, HC subclass, found in Saccharomyces cerevisiae POB3/SPT16 histone-associated protein 1 (ScPSH1) and similar proteins; ScPSH1 is a Cse4-specific E3 ubiquitin ligase that interacts with the kinetochore protein Pat1 and targets the degradation of budding yeast centromeric histone H3 variant, CENP-ACse4, which is essential for faithful chromosome segregation. ScPSH1 contains a C3HC4-type RING-HC finger and a DNA directed RNA polymerase domain.


Pssm-ID: 438230 [Multi-domain]  Cd Length: 54  Bit Score: 53.14  E-value: 3.26e-09
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                 ....*....|....*....|....*....|....*....|....*....|...
gi 124430766 728 LEQSFMCVCCQELVYQPVTTECFHNVCKDCLQRSFKAQV-FSCPACRHDLGQN 779
Cdd:cd16568    1 ILETQECIICHEYLYEPMVTTCGHTYCYTCLNTWFKSNRsLSCPDCRTKITTQ 53
PHD1_KDM5B cd15603
PHD finger 1 found in lysine-specific demethylase 5B (KDM5B); KDM5B (also termed Cancer/testis ...
348-393 1.06e-08

PHD finger 1 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), PLU-1, or retinoblastoma-binding protein 2 homolog 1 (RBP2-H1 or RBBP2H1A)) 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 pregnant females 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 first PHD finger.


Pssm-ID: 277076  Cd Length: 46  Bit Score: 51.49  E-value: 1.06e-08
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gi 124430766 348 CHKCGEKRDPNMQLLCDECNMAYHIYCLSPPLDKVPEEEyWYCPSC 393
Cdd:cd15603    2 CLVCGSGNDEDRLLLCDGCDDSYHTFCLIPPLHDVPKGD-WRCPKC 46
PHD2_d4 cd15530
PHD finger 2 found in d4 gene family proteins; The family includes proteins coded by three ...
347-393 1.74e-08

PHD finger 2 found in d4 gene family proteins; The family includes proteins coded by three members of the d4 gene family, DPF1 (neuro-d4), DPF2 (ubi-d4/Requiem), and DPF3 (cer-d4), which function as transcription factors and are involved in transcriptional regulation of genes by changing the condensed/decondensed state of chromatin in the nucleus. DPF2 is ubiquitously expressed and it acts as a transcription factor that may participate in developmentally programmed cell death. DPF1 and DPF3 are expressed predominantly in neural tissues, and they may be involved in the transcription regulation of neuro-specific gene clusters. The d4 family proteins show distinct domain organization with domain 2/3 in the N-terminal region, a Cys2His2 (C2H2) zinc finger or Kruppel-type zinc finger in the central part and two adjacent plant homeodomain (PHD) fingers (d4-domain) in the C-terminal part of the molecule. This model corresponds to the second PHD finger.


Pssm-ID: 277005  Cd Length: 46  Bit Score: 50.85  E-value: 1.74e-08
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gi 124430766 347 SCHKCGEKRDPNMQLLCDECNMAYHIYCLSPPLDKVPEEEyWYCPSC 393
Cdd:cd15530    1 SCSLCGTSENDDQLLFCDDCDRGYHMYCLSPPMSEPPEGS-WSCHLC 46
PHD2_PHF12_Rco1 cd15534
PHD finger 2 found in PHD finger protein 12 (PHF12), yeast Rco1, and similar proteins; PHF12, ...
348-391 1.92e-08

PHD finger 2 found in PHD finger protein 12 (PHF12), yeast Rco1, and similar proteins; 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 subfamily also includes yeast 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 PHD fingers, which are required for the methylation of histone H3 lysine 36 (H3K36) nucleosome recognition by Rpd3S. This model corresponds to the second PHD finger.


Pssm-ID: 277009  Cd Length: 47  Bit Score: 50.81  E-value: 1.92e-08
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gi 124430766 348 CHKCGEKRDPNMQLLCDECNMAYHIYCLSPPLDKVPEEEYWYCP 391
Cdd:cd15534    2 CFKCNRSCRVAPLIQCDYCPLLFHLDCLDPPLTHPPATGRWMCP 45
RING-HC_RNF168 cd16550
RING finger, HC subclass, found in RING finger protein 168 (RNF168) and similar proteins; ...
734-773 2.06e-08

RING finger, HC subclass, found in RING finger protein 168 (RNF168) and similar proteins; RNF168 is an E3 ubiquitin-protein ligase that promotes noncanonical K27 ubiquitination to signal DNA damage. It, together with RNF8, functions as a DNA damage response (DDR) factor that promotes a series of ubiquitylation events on substrates, such as H2A and H2AX with H2AK13/15 ubiquitylation, facilitates recruitment of repair factors p53-binding protein 1 (53BP1) or the RAP80-BRCA1 complex to sites of double-strand breaks (DSBs), and inhibits homologous recombination (HR) in cells deficient in the tumor suppressor BRCA1. RNF168 also promotes H2A neddylation, which antagonizes ubiquitylation of H2A and regulates DNA damage repair. Moreover, RNF168 forms a functional complex with RAD6A or RAD6B during the DNA damage response. RNF168 contains an N-terminal C3HC4-type RING-HC finger that catalyzes H2A-K15ub and interacts with H2A, and two MIU (motif interacting with ubiquitin) domains responsible for the interaction with K63 linked poly-ubiquitin.


Pssm-ID: 438212 [Multi-domain]  Cd Length: 48  Bit Score: 50.84  E-value: 2.06e-08
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gi 124430766 734 CVC--CQELVYQPVTTECFHNVCKDCLQRSFKAQVFSCPACR 773
Cdd:cd16550    1 CLCpiCLEILVEPVTLPCNHTLCMPCFQSTVEKASLCCPLCR 42
PHD_SF cd15489
PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) ...
347-393 2.82e-08

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: 50.39  E-value: 2.82e-08
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gi 124430766 347 SCHKCGEKRDPNMQLL-CDECNMAYHIYCLSPPLDKVPEEEYWYCPSC 393
Cdd:cd15489    1 SCIVCGKGGDLGGELLqCDGCGKWFHADCLGPPLSSFVPNGKWICPVC 48
PHD2_PHF14 cd15562
PHD finger 2 found in PHD finger protein 14 (PHF14) and similar proteins; PHF14 is a novel ...
347-393 3.36e-08

PHD finger 2 found in PHD finger protein 14 (PHF14) and similar proteins; PHF14 is a novel nuclear transcription factor that controls the proliferation of mesenchymal cells by directly repressing platelet-derived growth factor receptor-alpha (PDGFRalpha) expression. It also acts as an epigenetic regulator and plays an important role in the development of multiple organs in mammals. PHF14 contains three canonical plant homeodomain (PHD) fingers and a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His. It can interact with histones through its PHD fingers. The model corresponds to the second PHD finger.


Pssm-ID: 277037  Cd Length: 50  Bit Score: 50.10  E-value: 3.36e-08
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gi 124430766 347 SCHKCGEKRDPNMQLLCDECNMAYHIYCLSPPLDKVPEEE---YWYCPSC 393
Cdd:cd15562    1 SCGICKKSNDQHLLALCDTCKLYYHLGCLDPPLTRMPKKTknsGWQCSEC 50
PHD1_MTF2_PHF19_like cd15499
PHD finger 1 found in polycomb repressive complex 2 (PRC2)-associated polycomb-like (PCL) ...
342-393 4.97e-08

PHD finger 1 found in polycomb repressive complex 2 (PRC2)-associated polycomb-like (PCL) family proteins MTF2, PHF19, and similar proteins; The family includes two PCL family proteins, metal-response element-binding transcription factor 2 (MTF2/PCL2) and PHF19/PCL3, which are homologs of PHD finger protein1 (PHF1). PCL family proteins are accessory components of the polycomb repressive complex 2 (PRC2) core complex and all contain an N-terminal Tudor domain followed by two PHD fingers, and a C-terminal MTF2 domain. They specifically recognize tri-methylated H3K36 (H3K36me3) through their N-terminal Tudor domains. The interaction between their Tudor domains and H3K36me3 is critical for both the targeting and spreading of PRC2 into active chromatin regions and for the maintenance of optimal repression of poised developmental genes where PCL proteins, H3K36me3, and H3K27me3 coexist. Moreover, unlike other PHD finger-containing proteins, the first PHD fingers of PCL proteins do not display histone H3K4 binding affinity and they do not affect the Tudor domain binding to histones. This model corresponds to the first PHD finger.


Pssm-ID: 276974  Cd Length: 53  Bit Score: 49.81  E-value: 4.97e-08
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gi 124430766 342 TCHMCschKCGEKRDPNMQLLCDECNMAYHIYCLSPPLDKVP--EEEYWYCPSC 393
Cdd:cd15499    1 TCSIC---GGAEARDGNEILICDKCDKGYHQLCHSPKVRTSPleGDEKWFCSRC 51
RING-HC_LONFs_rpt2 cd16514
second RING finger, HC subclass, found in the LON peptidase N-terminal domain and RING finger ...
731-776 5.31e-08

second RING finger, HC subclass, found in the LON peptidase N-terminal domain and RING finger protein family; The LON peptidase N-terminal domain and RING finger protein family includes LONRF1 (also known as RING finger protein 191 or RNF191), LONRF2 (also known as RING finger protein 192, RNF192, or neuroblastoma apoptosis-related protease), LONRF3 (also known as RING finger protein 127 or RNF127), which are characterized by containing two C3HC4-type RING-HC fingers, four tetratricopeptide (TPR) repeats, and an ATP-dependent protease La (LON) substrate-binding domain at the C-terminus. Their biological functions remain unclear. This model corresponds to the second RING-HC finger.


Pssm-ID: 438177 [Multi-domain]  Cd Length: 45  Bit Score: 49.57  E-value: 5.31e-08
                         10        20        30        40
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gi 124430766 731 SFMCVCCQELVYQPVTTECFHNVCKDCLQRSFkAQVFSCPACRHDL 776
Cdd:cd16514    1 DLECSLCLRLLYEPVTTPCGHTFCRACLERCL-DHSPKCPLCRTSL 45
PHD1_KDM5C_5D cd15604
PHD finger 1 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D); The family ...
348-393 6.36e-08

PHD finger 1 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D); The family includes KDM5C and KDM5D, both of which belong to the JARID subfamily within the JmjC proteins. KDM5C (also termed Histone demethylase JARID1C, Jumonji/ARID domain-containing protein 1C, SmcX, or Xe169) 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 (also termed Histocompatibility Y antigen (H-Y), Histone demethylase JARID1D, Jumonji/ARID domain-containing protein 1D, or SmcY) is a male-specific antigen that shows a demethylase activity specific for di- and tri-methylated histone H3K4 (H3K4me3 andH3K4me2), 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. Both KDM5C and KDM5D 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 plant homeodomain (PHD) fingers. This model corresponds to the first PHD finger.


Pssm-ID: 277077  Cd Length: 46  Bit Score: 49.45  E-value: 6.36e-08
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gi 124430766 348 CHKCGEKRDPNMQLLCDECNMAYHIYCLSPPLDKVPeEEYWYCPSC 393
Cdd:cd15604    2 CRMCSRGDEDDKLLLCDGCDDNYHTFCLLPPLPEPP-KGIWRCPKC 46
PHD1_KDM5A cd15602
PHD finger 1 found in Lysine-specific demethylase 5A (KDM5A); KDM5A (also termed Histone ...
348-393 8.26e-08

PHD finger 1 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 first PHD finger.


Pssm-ID: 277075  Cd Length: 49  Bit Score: 49.18  E-value: 8.26e-08
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gi 124430766 348 CHKCGEKRDPNMQLLCDECNMAYHIYCLSPPLDKVPEEEyWYCPSC 393
Cdd:cd15602    2 CLFCGRGNNEDKLLLCDGCDDSYHTFCLIPPLPDVPKGD-WRCPKC 46
PHD1_AIRE cd15539
PHD finger 1 found in autoimmune regulator (AIRE); AIRE, also termed autoimmune ...
361-393 1.08e-07

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: 48.60  E-value: 1.08e-07
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                 ....*....|....*....|....*....|...
gi 124430766 361 LLCDECNMAYHIYCLSPPLDKVPEEEyWYCPSC 393
Cdd:cd15539   12 LCCDGCPRAFHLACLVPPLTLIPSGT-WRCSSC 43
PHD2_KAT6A_6B cd15527
PHD finger 2 found in monocytic leukemia zinc-finger protein (MOZ) and its factor (MORF); MOZ, ...
348-393 1.13e-07

PHD finger 2 found in monocytic leukemia zinc-finger protein (MOZ) and its factor (MORF); MOZ, also termed histone acetyltransferase KAT6A, YBF2/SAS3, SAS2 and TIP60 protein 3 (MYST-3), or runt-related transcription factor-binding protein 2, or zinc finger protein 220, is a MYST-type histone acetyltransferase (HAT) that functions as a coactivator for acute myeloid leukemia 1 protein (AML1)- and p53-dependent transcription. It possesses intrinsic HAT activity to acetylate both itself and lysine (K) residues on histone H2B, histone H3 (K14) and histone H4 (K5, K8, K12 and K16) in vitro and H3K9 in vivo. MOZ-related factor (MORF), also termed MOZ2, or histone acetyltransferase KAT6B, or MOZ, YBF2/SAS3, SAS2 and TIP60 protein 4 (MYST4), is a ubiquitously expressed transcriptional regulator with intrinsic HAT activity. It can interact with the Runt-domain transcription factor Runx2 and form a tetrameric complex with BRPFs, ING5, and EAF6. Both MOZ and MORF are catalytic subunits of HAT complexes that are required for normal developmental programs, such as hematopoiesis, neurogenesis, and skeletogenesis, and are also implicated in human leukemias. MOZ is also the catalytic subunit of a tetrameric inhibitor of growth 5 (ING5) complex, which specifically acetylates nucleosomal histone H3K14. Moreover, MOZ and MORF are involved in regulating transcriptional activation mediated by Runx2 (or Cbfa1), a Runt-domain transcription factor known to play important roles in T cell lymphomagenesis and bone development, and its homologs. MOZ contains a linker histone 1 and histone 5 domains and two plant homeodomain (PHD) fingers. In contrast, MORF contains an N-terminal region containing two PHD fingers, a putative HAT domain, an acidic region, and a C-terminal Ser/Met-rich domain. The family corresponds to the first PHD finger.


Pssm-ID: 277002  Cd Length: 46  Bit Score: 48.53  E-value: 1.13e-07
                         10        20        30        40
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gi 124430766 348 CHKCGEKRDPNMQLLCDECNMAYHIYCLSPPLDKVPEEEyWYCPSC 393
Cdd:cd15527    2 CSVCQDSGNADNLLFCDACDKGFHMECHDPPLTRMPKGK-WVCQIC 46
RING-HC_TRIM36_C-I cd16756
RING finger, HC subclass, found in tripartite motif-containing protein 36 (TRIM36) and similar ...
729-776 1.18e-07

RING finger, HC subclass, found in tripartite motif-containing protein 36 (TRIM36) and similar proteins; TRIM36, the human ortholog of mouse Haprin, also known as RING finger protein 98 (RNF98) or zinc-binding protein Rbcc728, is an E3 ubiquitin-protein ligase expressed in the germ plasm. It has been implicated in acrosome reaction, fertilization, and embryogenesis, as well as in carcinogenesis. TRIM36 functions upstream of Wnt/beta-catenin activation, and plays a role in controlling the stability of proteins regulating microtubule polymerization during cortical rotation, and subsequently dorsal axis formation. It is also potentially associated with chromosome segregation by interacting with the kinetochore protein centromere protein-H (CENP-H), and colocalizing with the microtubule protein alpha-tubulin. Its overexpression may cause chromosomal instability and carcinogenesis. It is, thus, a novel regulator affecting cell cycle progression. Moreover, TRIM36 plays a critical role in the arrangement of somites during embryogenesis. TRIM36 belongs to the C-I subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox2, and a coiled coil region, as well as a COS (carboxyl-terminal subgroup one signature) box, a fibronectin type III (FN3) domain, a PRY domain and a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain.


Pssm-ID: 438414 [Multi-domain]  Cd Length: 49  Bit Score: 48.76  E-value: 1.18e-07
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                 ....*....|....*....|....*....|....*....|....*...
gi 124430766 729 EQSFMCVCCQELVYQPVTTECFHNVCKDCLQRSFKaqVFSCPACRHDL 776
Cdd:cd16756    1 ERELICPSCKELFTHPLILPCQHSVCHKCVKELLT--TFPCPGCQHDV 46
PHD1_Snt2p_like cd15497
PHD finger 1 found in Saccharomyces cerevisiae SANT domain-containing protein 2 (Snt2p) and ...
347-393 1.68e-07

PHD finger 1 found in Saccharomyces cerevisiae SANT domain-containing protein 2 (Snt2p) and similar proteins; Snt2p is a yeast protein that may function in multiple stress pathways. It coordinates the transcriptional response to hydrogen peroxide-mediated oxidative stress through interaction with Ecm5 and the Rpd3 deacetylase. Snt2p contains a bromo adjacent homology (BAH) domain, two canonical Cys4HisCys3 plant homeodomain (PHD) fingers, a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, and a SANT (SWI3, ADA2, N-CoR and TFIIIB) DNA-binding domain; this model corresponds to the first canonical Cys4HisCys3 PHD finger.


Pssm-ID: 276972  Cd Length: 48  Bit Score: 48.07  E-value: 1.68e-07
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 124430766 347 SCHKCGEKRDPNMQLLCDECNMAYHIYCLSPPLDKVPEEEY-WYCPSC 393
Cdd:cd15497    1 SCKVCKEWCASDDSVRCDECKVSYHLLCVDPPLTKKPNRGFvWSCAPC 48
PHD2_KMT2D cd15595
PHD finger 2 found in Histone-lysine N-methyltransferase 2D (KMT2D); KMT2D, also termed ...
348-393 2.07e-07

PHD finger 2 found in Histone-lysine N-methyltransferase 2D (KMT2D); KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named myeloid/lymphoid or mixed-lineage leukemia 4 (MLL4), a fourth human homolog of Drosophila trithorax, located on chromosome 12. KMT2D enzymatically generates trimethylated histone H3 Lys 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such asHOXA1-3 and NESTIN. It is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and KMT2D. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D contains the catalytic domain SET, five plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions. This model corresponds to the second PHD finger.


Pssm-ID: 277070  Cd Length: 46  Bit Score: 48.07  E-value: 2.07e-07
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 124430766 348 CHKCGEKRDPNMQLLCDECNMAYHIYCLSPPLDKVPEEEyWYCPSC 393
Cdd:cd15595    2 CQTCRKPGEDSKMLVCEACDKGYHTFCLKPAMESLPTDS-WKCKAC 46
Ubl_ubiquitin cd01803
ubiquitin-like (Ubl) domain found in ubiquitin; Ubiquitin is a protein modifier in eukaryotes ...
1-74 2.50e-07

ubiquitin-like (Ubl) domain found in ubiquitin; Ubiquitin is a protein modifier in eukaryotes that is involved in various cellular processes, including transcriptional regulation, cell cycle control, and DNA repair. Ubiquitination is comprised of a cascade of E1, E2 and E3 enzymes that results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. Ubiquitin-like (Ubl) proteins have similar ubiquitin beta-grasp fold and attach to other proteins in a Ubl manner but with biochemically distinct roles. Ubiquitin (Ub)and Ubl proteins conjugate and deconjugate via ligases and peptidases to covalently modify target polypeptides. Ub includes Ubq/RPL40e and Ubq/RPS27a fusions as well as homopolymeric multiubiquitin protein chains.


Pssm-ID: 340501 [Multi-domain]  Cd Length: 76  Bit Score: 48.59  E-value: 2.50e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 124430766   1 MWIQVRTIDGsQTRTIeDVSRKATIEELRERVWALFDVRPECQRLFYRGKQLENGYTLFDYDVGLNDIIQLLVR 74
Cdd:cd01803    1 MQIFVKTLTG-KTITL-EVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLR 72
PHD2_KMT2C cd15594
PHD finger 2 found in Histone-lysine N-methyltransferase 2C (KMT2C); KMT2C, also termed ...
348-393 3.15e-07

PHD finger 2 found in Histone-lysine N-methyltransferase 2C (KMT2C); KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3) or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2C contains several plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, an ATPase alpha beta signature, a high mobility group (HMG)-1 box, a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain and two FY (phenylalanine tyrosine)-rich domains. This model corresponds to the second PHD finger.


Pssm-ID: 277069  Cd Length: 46  Bit Score: 47.63  E-value: 3.15e-07
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 124430766 348 CHKCGEKRDPNMQLLCDECNMAYHIYCLSPPLDKVPEEEyWYCPSC 393
Cdd:cd15594    2 CQTCRQPGDDNKMLVCDTCDKGYHTFCLQPVMTTIPKNG-WKCKNC 46
Ubl2_ISG15 cd01810
ubiquitin-like (Ubl) domain 2 found in interferon-stimulated gene 15 (ISG15) and similar ...
1-63 3.26e-07

ubiquitin-like (Ubl) domain 2 found in interferon-stimulated gene 15 (ISG15) and similar proteins; ISG15, also termed interferon-induced 15 kDa protein, or interferon-induced 17 kDa protein (IP17), or ubiquitin cross-reactive protein (UCRP), is an antiviral interferon-induced ubiquitin-like protein that upon viral infection it modifies cellular and viral proteins by mechanisms similar to ubiquitination. Although ISG15 has properties similar to those of other ubiquitin-like (Ubl) molecules, it is a unique member of the Ubl superfamily, whose expression and conjugation to target proteins are tightly regulated by specific signaling pathways, indicating it may have specialized functions in the immune system. ISG15 contains two tandem Ubl domains with a beta-grasp Ubl fold. This family corresponds to the second Ubl domain.


Pssm-ID: 340508 [Multi-domain]  Cd Length: 74  Bit Score: 48.22  E-value: 3.26e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 124430766   1 MWIQVRTIDGsQTRTIeDVSRKATIEELRERVWALFDVRPECQRLFYRGKQLENGYTLFDYDV 63
Cdd:cd01810    1 LSIFVRNEKG-QSHTY-EVRLTQTVDQLKQKVSGREGVHDDQFWLTFEGRPLEDQLPLGEYGL 61
RING-HC_RNF125 cd16542
RING finger, HC subclass, found in RING finger protein 125 (RNF125); RNF125, also known as ...
731-773 3.99e-07

RING finger, HC subclass, found in RING finger protein 125 (RNF125); RNF125, also known as T-cell RING activation protein 1 (TRAC-1), is an E3 ubiquitin-protein ligase that is predominantly expressed in lymphoid cells, and functions as a positive regulator of T cell activation. It also down-modulates HIV replication and inhibits pathogen-induced cytokine production. It negatively regulates type I interferon signaling, which conjugates Lys(48)-linked ubiquitination to retinoic acid-inducible gene-I (RIG-I) and subsequently leads to the proteasome-dependent degradation of RIG-I. Further, RNF125 conjugates ubiquitin to melanoma differentiation-associated gene 5 (MDA5), a family protein of RIG-I. It thus acts as a negative regulator of RIG-I signaling, and is a direct target of miR-15b in the context of Japanese encephalitis virus (JEV) infection. Moreover, RNF125 binds to and ubiquitinates JAK1, prompting its degradation and inhibition of receptor tyrosine kinase (RTK) expression. It also negatively regulates p53 function through physical interaction and ubiquitin-mediated proteasome degradation. Mutations in RNF125 may lead to overgrowth syndromes (OGS). RNF125, together with three closely related proteins: RNF114, RNF138 and RNF166, forms a novel family of ubiquitin ligases with a C3HC4-type RING-HC finger, a C2HC-, and two C2H2-type zinc fingers, as well as a ubiquitin interacting motif (UIM). The UIM of RNF125 binds K48-linked poly-ubiquitin chains and is, together with the RING domain, required for auto-ubiquitination.


Pssm-ID: 438204 [Multi-domain]  Cd Length: 50  Bit Score: 47.18  E-value: 3.99e-07
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 124430766 731 SFMCVCCQELVYQPVTTECFHNVCKDCLQRSFKAQVFSCPACR 773
Cdd:cd16542    1 NFDCAVCLEVLHQPVRTRCGHVFCRPCIATSLRNNTWTCPYCR 43
PHD_BAZ2A cd15629
PHD finger found in bromodomain adjacent to zinc finger domain protein 2A (BAZ2A); BAZ2A, also ...
347-393 4.09e-07

PHD finger found in bromodomain adjacent to zinc finger domain protein 2A (BAZ2A); BAZ2A, also termed transcription termination factor I-interacting protein 5 (TTF-I-interacting protein 5, or Tip5), or WALp3, is an epigenetic regulator. It has been implicated in epigenetic rRNA gene silencing, as the large subunit of the SNF2h-containing chromatin-remodeling complex NoRC that induces nucleosome sliding in an ATP- and histone H4 tail-dependent fashion. BAZ2A has also been shown to be broadly overexpressed in prostate cancer, to regulate numerous protein-coding genes and to cooperate with EZH2 (enhancer of zeste homolog 2) to maintain epigenetic silencing at genes repressed in prostate cancer metastasis. Its overexpression is tightly associated with a prostate cancer subtype displaying CpG island methylator phenotype (CIMP) in tumors and with prostate cancer recurrence in patients. It contains a TAM (TIP5/ARBP/MBD) domain, a DDT domain, four AT-hooks, BAZ 1 and BAZ 2 motifs, a WAKZ (WSTF/Acf1/KIAA0314/ZK783.4) motif, a plant homeodomain (PHD) finger, and a bromodomain.


Pssm-ID: 277099  Cd Length: 47  Bit Score: 47.15  E-value: 4.09e-07
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 124430766 347 SCHKCGEKRDPNMQLLCDECNMAYHIYCLSPPLDKVPEEEyWYCPSC 393
Cdd:cd15629    1 TCLVCRKGDNDEYLLLCDGCDRGCHMYCHRPKMLQVPEGD-WFCPNC 46
RING-HC_BAR cd16497
RING finger, HC subclass, found in bifunctional apoptosis regulator (BAR); BAR, also known as ...
731-773 5.87e-07

RING finger, HC subclass, found in bifunctional apoptosis regulator (BAR); BAR, also known as RING finger protein 47, was originally identified as an inhibitor of Bax-induced apoptosis. It participates in the block of apoptosis induced by TNF-family death receptors (extrinsic pathway) and mitochondria-dependent apoptosis (intrinsic pathway). BAR is predominantly expressed by neurons in the central nervous system and is involved in the regulation of neuronal survival. It is an endoplasmic reticulum (ER)-associated RING-type E3 ubiquitin ligase that interacts with BI-1 protein and post-translationally regulates its stability, as well as functioning in ER stress. BAR contains an N-terminal C3HC4-type RING-HC finger, a SAM domain, a coiled-coil domain, and a C-terminal transmembrane (TM) domain. This model corresponds to the RING-HC finger responsible for the binding of ubiquitin conjugating enzymes (E2s).


Pssm-ID: 438160 [Multi-domain]  Cd Length: 52  Bit Score: 46.73  E-value: 5.87e-07
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 124430766 731 SFMCVCCQELVYQPVTTECFHNVCKDCLQRSFKA-QVFSCPACR 773
Cdd:cd16497    1 EFLCHCCYDLLVNPTTLNCGHSFCRHCLALWWKSsKKTECPECR 44
PHD1_BPTF cd15559
PHD finger 1 found in bromodomain and PHD finger-containing transcription factor (BPTF); BPTF, ...
344-393 5.90e-07

PHD finger 1 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 first PHD finger.


Pssm-ID: 277034 [Multi-domain]  Cd Length: 43  Bit Score: 46.64  E-value: 5.90e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 124430766 344 HMCSCHKCGEkrdpnmQLLCDECNMAYHIYCLSPPLDKVPEEEyWYCPSC 393
Cdd:cd15559    1 HCRVCHKLGD------LLCCETCSAVYHLECVDPPLEEVPEED-WQCEVC 43
PHD3_PHF14 cd15563
PHD finger 3 found in PHD finger protein 14 (PHF14) and similar proteins; PHF14 is a novel ...
347-393 8.57e-07

PHD finger 3 found in PHD finger protein 14 (PHF14) and similar proteins; PHF14 is a novel nuclear transcription factor that controls the proliferation of mesenchymal cells by directly repressing platelet-derived growth factor receptor-alpha (PDGFRalpha) expression. It also acts as an epigenetic regulator and plays an important role in the development of multiple organs in mammals. PHF14 contains three canonical plant homeodomain (PHD) fingers and a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His. It can interact with histones through its PHD fingers. The model corresponds to the third PHD finger.


Pssm-ID: 277038  Cd Length: 49  Bit Score: 46.23  E-value: 8.57e-07
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 124430766 347 SCHKCGEKRDPNMQLLCDECNMAYHIYCLSPPLDKVPEEEY--WYCPSC 393
Cdd:cd15563    1 ECCVCKQTGDNSQLVRCDECKLCYHFGCLDPPLKKSPKQRGygWVCEEC 49
RING-HC_ORTHRUS_rpt1 cd23138
first RING finger, HC subclass, found in Arabidopsis thaliana ORTHRUS and similar proteins; ...
731-773 1.10e-06

first RING finger, HC subclass, found in Arabidopsis thaliana ORTHRUS and similar proteins; This subfamily includes Arabidopsis thaliana ORTHRUS 1-5. They are E3 ubiquitin-protein ligases that may participate in CpG methylation-dependent transcriptional regulation and/or epigenetic transcriptional silencing. ORTHRUS 1 mediates ubiquitination with the E2 ubiquitin-conjugating enzymes UBC11, UBC8 and UBC8 homologs (e.g. UBC10, UBC11, UBC28 and UBC29) but not with UBC27, UBC30, UBC32, UBC34 and UBC36. ORTHRUS 2 and 5 mediate ubiquitination with the E2 ubiquitin-conjugating enzyme UBC11. ORTHRUS 1 and 2 promote methylation-mediated gene silencing leading, for example, to early flowering. They can bind to CpG, CpNpG, and CpNpN DNA motifs, with a strong preference for methylated forms, and with highest affinity for CpG substrates. Members of this subfamily contain two typical C3HC4-type RING-HC fingers. This model corresponds to the first one.


Pssm-ID: 438500 [Multi-domain]  Cd Length: 48  Bit Score: 45.90  E-value: 1.10e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 124430766 731 SFMCVCCQELVYQPVTTECFHNVCKDCLQRSFKAQVFSCPACR 773
Cdd:cd23138    2 ELNCSFCMQLPERPVTTPCGHNFCLKCFQKWMGQGKKTCGTCR 44
Ubl_UBL4A_like cd01807
ubiquitin-like (Ubl) domain found in ubiquitin-like proteins UBL4A and similar proteins; UBL4A, ...
1-74 1.22e-06

ubiquitin-like (Ubl) domain found in ubiquitin-like proteins UBL4A and similar proteins; UBL4A, also termed GdX, is a ubiquitously expressed ubiquitin-like (Ubl) protein that forms a complex with partner proteins and participates in the protein processing through endoplasmic reticulum (ER), acting as a chaperone. As a key component of the BCL2-associated athanogene 6 (BAG6) chaperone complex, UBL4A plays a role in mediating DNA damage signaling and cell death. UBL4A also regulates insulin-induced Akt plasma membrane translocation through promotion of Arp2/3-dependent actin branching. Moreover, UBL4A specifically stabilizes the TC45/STAT3 association and promotes dephosphorylation of STAT3 to repress tumorigenesis. UBL4B is testis-specific, and encoded by an X-derived retrogene Ubl4b, which is specifically expressed in post-meiotic germ cells in mammals. As a germ cell-specific cytoplasmic protein, UBL4B is not present in somatic cells. Moreover, UBL4B is present in elongated spermatids, but not in spermatocytes and round spermatids, suggesting its function is restricted to late spermiogenesis. The function of UBL4A may be compensated by either UBL4B or other Ubl proteins in normal conditions. Both UBL4A and UBL4B contain a conserved Ubl domain with a beta-grasp Ubl fold, a common structure involved in protein-protein interactions.


Pssm-ID: 340505 [Multi-domain]  Cd Length: 72  Bit Score: 46.59  E-value: 1.22e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 124430766   1 MWIQVRTIDGSQTrTIEdVSRKATIEELRERVWALFDVRPECQRLFYRGKQLENGYTLFDYDVGLNDIIQLLVR 74
Cdd:cd01807    1 MLITVKILQGKEC-TIE-VSPTESVLTVKQLVAEQLNVPVSQQRLVFKGKTLADEHSLSDYSIGPGSKIHLVVK 72
RING smart00184
Ring finger; E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and ...
734-772 1.23e-06

Ring finger; E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s)


Pssm-ID: 214546 [Multi-domain]  Cd Length: 40  Bit Score: 45.58  E-value: 1.23e-06
                           10        20        30
                   ....*....|....*....|....*....|....*....
gi 124430766   734 CVCCQELVYQPVTTECFHNVCKDCLQRSFKAQVFSCPAC 772
Cdd:smart00184   2 PICLEEYLKDPVILPCGHTFCRSCIRKWLESGNNTCPIC 40
PHD1_CHD_II cd15531
PHD finger 1 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins; Class II CHD ...
361-393 1.41e-06

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: 45.67  E-value: 1.41e-06
                         10        20        30
                 ....*....|....*....|....*....|...
gi 124430766 361 LLCDECNMAYHIYCLSPPLDKVPEEEyWYCPSC 393
Cdd:cd15531   12 ILCDTCPRAYHLVCLDPELEKAPEGK-WSCPHC 43
RING-HC_TRIM4_C-IV cd16590
RING finger, HC subclass, found in tripartite motif-containing protein TRIM4 and similar ...
726-774 1.71e-06

RING finger, HC subclass, found in tripartite motif-containing protein TRIM4 and similar proteins; TRIM4 belongs to the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox2, and a coiled coil region, as well as a SPRY/B30.2 domain positioned C-terminal to the RBCC domain. TRIM4, also known as RING finger protein 87 (RNF87), is a cytoplasmic E3 ubiquitin-protein ligase that has recently evolved and is present only in higher mammals. It transiently interacts with mitochondria, induces mitochondrial aggregation and sensitizes the cells to hydrogen peroxide (H2O2) induced death. Its interaction with peroxiredoxin 1 (PRX1) is critical for the regulation of H2O2 induced cell death. Moreover, TRIM4 functions as a positive regulator of RIG-I-mediated type I interferon induction. It regulates the K63-linked ubiquitination of RIG-1 and assembly of antiviral signaling complex at the mitochondria.


Pssm-ID: 438252 [Multi-domain]  Cd Length: 61  Bit Score: 45.79  E-value: 1.71e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 124430766 726 KKLEQSFMCVCCQELVYQPVTTECFHNVCKDCLQRSFK--AQVFSCPACRH 774
Cdd:cd16590    1 EDIQEELTCPICLDYFQDPVSIECGHNFCRGCLHRNWApgGGPFPCPECRH 51
RING-HC_TRIM72_C-IV cd16612
RING finger, HC subclass, found in tripartite motif-containing protein 72 (TRIM72) and similar ...
728-773 1.78e-06

RING finger, HC subclass, found in tripartite motif-containing protein 72 (TRIM72) and similar proteins; TRIM72, also known as Mitsugumin-53 (MG53), is a muscle-specific protein that plays a central role in cell membrane repair by nucleating the assembly of the repair machinery at muscle injury sites. It is required in repair of alveolar epithelial cells under plasma membrane stress failure. It interacts with dysferlin to regulate sarcolemmal repair. Upregulation of TRIM72 develops obesity, systemic insulin resistance, dyslipidemia, and hyperglycemia, as well as induces diabetic cardiomyopathy through transcriptional activation of the peroxisome proliferation-activated receptor alpha (PPAR-alpha) signaling pathway. Compensation for the absence of AKT signaling by ERK signaling during TRIM72 overexpression leads to pathological hypertrophy. Moreover, TRIM72 functions as a novel negative feedback regulator of myogenesis by targeting insulin receptor substrate-1 (IRS-1). It is transcriptionally activated by the synergism of myogenin (MyoD) and myocyte enhancer factor 2 (MEF2). TRIM72 belongs to the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain.


Pssm-ID: 438274 [Multi-domain]  Cd Length: 60  Bit Score: 45.88  E-value: 1.78e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 124430766 728 LEQSFMCVCCQELVYQPVTTECFHNVCKDCLQRSFK---AQVFSCPACR 773
Cdd:cd16612    1 MHQDLSCPLCLKLFQSPVTTECGHTFCQDCLSRVPKeedGGSTSCPTCQ 49
RING-HC_RNF138 cd16544
RING finger, HC subclass, found in RING finger protein 138 (RNF138) and similar proteins; ...
730-773 2.39e-06

RING finger, HC subclass, found in RING finger protein 138 (RNF138) and similar proteins; RNF138, also known as Nemo-like kinase-associated RING finger protein (NARF) or NLK-associated RING finger protein, is an E3 ubiquitin-protein ligase that plays an important role in glioma cell proliferation, apoptosis, and cell cycle. It specifically cooperates with the E2 conjugating enzyme E2-25K (Hip-2/UbcH1), regulates the ubiquitylation and degradation of T cell factor/lymphoid enhancer factor (TCF/LEF), and further suppresses Wnt-beta-catenin signaling. RNF138, together with three closely related proteins: RNF114, RNF125 and RNF166, forms a novel family of ubiquitin ligases with a C3HC4-type RING-HC finger, a C2HC-, and two C2H2-type zinc fingers, as well as a ubiquitin interacting motif (UIM).


Pssm-ID: 438206 [Multi-domain]  Cd Length: 53  Bit Score: 45.09  E-value: 2.39e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 124430766 730 QSFMCVCCQELVYQPVTTE-CFHNVCKDCLQRSFKAQVFSCPACR 773
Cdd:cd16544    1 AELTCPVCQEVLKDPVELPpCRHIFCKACILLALRSSGARCPLCR 45
PHD_PHF21A cd15523
PHD finger found in PHD finger protein 21A (PHF21A); PHF21A (also termed BHC80a or BRAF35-HDAC ...
346-393 2.74e-06

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: 44.69  E-value: 2.74e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 124430766 346 CSCHKCGEkrdpnmQLLCDECNMAYHIYCLSPPLDKVPeEEYWYCPSC 393
Cdd:cd15523    3 SVCRKSGE------LLMCDTCSLVYHLDCLDPPLKTIP-KGMWICPKC 43
Ubl_BAG6 cd01809
ubiquitin-like (Ubl) domain found in BCL2-associated athanogene 6 (BAG6) and similar proteins; ...
3-74 3.06e-06

ubiquitin-like (Ubl) domain found in BCL2-associated athanogene 6 (BAG6) and similar proteins; BAG6, also termed large proline-rich protein BAG6, or BAG family molecular chaperone regulator 6, or HLA-B-associated transcript 3 (Bat3), or protein Scythe, or protein G3, is a nucleo-cytoplasmic shuttling chaperone protein that is highly conserved in eukaryotes. It functions in two distinct biological pathways, ubiquitin-mediated protein degradation of defective polypeptides and tail-anchored transmembrane protein biogenesis in mammals. BAG6 is a component of the heterotrimeric BAG6 sortase complex composed of BAG6, transmembrane recognition complex 35 (TRC35) and ubiquitin-like protein 4A (UBL4A). The BAG6 complex together with the cochaperone small, glutamine-rich, tetratricopeptide repeat-containing, protein alpha (SGTA) plays a role in the biogenesis of tail-anchored membrane proteins and subsequently shown to regulate the ubiquitination and proteasomal degradation of mislocalized proteins. Moreover, BAG6 acts as an apoptotic regulator that binds reaper, a potent apoptotic inducer. BAG6/reaper is thought to signal apoptosis, in part through regulating the folding and activity of apoptotic signaling molecules. It is also likely a key regulator of the molecular chaperone Heat Shock Protein A2 (HSPA2) stability/function in human germ cells. Furthermore, aspartyl protease-mediated cleavage of BAG6 is necessary for autophagy and fungal resistance in plants. BAG6 contains a ubiquitin-like (Ubl) domain with a beta-grasp Ubl fold, which provides a platform for discriminating substrates with shorter hydrophobicity stretches as a signal for defective proteins.


Pssm-ID: 340507  Cd Length: 71  Bit Score: 45.41  E-value: 3.06e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 124430766   3 IQVRTIDgSQTRTIEdVSRKATIEELRERVWALFDVRPECQRLFYRGKQLENGYTLFDYDVGlNDIIQLLVR 74
Cdd:cd01809    3 VTVKTLD-SQNRTFT-VPEEITVKEFKEHIASSVNIPAEKQRLIFQGRVLQDDKKLKEYDVD-GKVIHLVER 71
RING-HC_TRIM40-C-V cd16583
RING finger, HC subclass, found in tripartite motif-containing protein 40 (TRIM40) and similar ...
733-780 3.07e-06

RING finger, HC subclass, found in tripartite motif-containing protein 40 (TRIM40) and similar proteins; TRIM40, also known as probable E3 NEDD8-protein ligase or RING finger protein 35 (RNF35), is highly expressed in the gastrointestinal tract including the stomach, small intestine, and large intestine. It enhances neddylation of inhibitor of nuclear factor kappaB kinase subunit gamma (IKKgamma), inhibits the activity of nuclear factor-kappaB (NF-kappaB)-mediated transcription, and thus prevents inflammation-associated carcinogenesis in the gastrointestinal tract. TRIM40 belongs to the C-V subclass of the TRIM (tripartite motif) family of proteins that are defined by an N-terminal RBCC (RING, Bbox, and coiled coil) domain, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as an uncharacterized region positioned C-terminal to the RBCC domain.


Pssm-ID: 438245 [Multi-domain]  Cd Length: 63  Bit Score: 45.21  E-value: 3.07e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 124430766 733 MCVCCQELVYQPVTTECFHNVCKDCLQRSFK----AQVFSCPACRHD-----LGQNY 780
Cdd:cd16583    7 VCPICQEPLKEAVSTDCGHLFCRMCLTQHAKkasaSGVFSCPVCRKPcsegvLGDGY 63
RING-HC_TRIM60-like_C-IV cd16607
RING finger, HC subclass, found in tripartite motif-containing proteins TRIM60, TRIM61, TRIM75 ...
734-774 3.79e-06

RING finger, HC subclass, found in tripartite motif-containing proteins TRIM60, TRIM61, TRIM75 and similar proteins; TRIM60, also known as RING finger protein 129 (RNF129) or RING finger protein 33 (RNF33), is a cytoplasmic protein expressed in the testis. It may play an important role in the spermatogenesis process, the development of the preimplantation embryo, and in testicular functions. RNF33 interacts with the cytoplasmic kinesin motor proteins KIF3A and KIF3B suggesting possible contribution to cargo movement along the microtubule in the expressed sites. It is also involved in spermatogenesis in Sertoli cells under the regulation of nuclear factor-kappaB (NF-kappaB). TRIM75 mainly localizes within spindles, suggesting it may function in spindle organization and thereby affect meiosis. Both TRIM60 and TRIM75 belong the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, a B2-box, and two coiled coil domains, as well as a PRY domain and a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain. In contrast, TRIM61 belongs to the C-V subclass of the TRIM family that contains RBCC domains only. Its biological function remains unclear.


Pssm-ID: 438269 [Multi-domain]  Cd Length: 48  Bit Score: 44.34  E-value: 3.79e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 124430766 734 CVCCQELVYQPVTTECFHNVCKDCLQRSFKAQ--VFSCPACRH 774
Cdd:cd16607    4 CPICLDYLKDPVTINCGHNFCRSCISMSWKDLqdTFPCPVCRF 46
RING-HC_PRT1-like cd23132
RING finger, HC subclass, found in Arabidopsis thaliana proteolysis 1 protein (PRT1) and ...
730-777 4.62e-06

RING finger, HC subclass, found in Arabidopsis thaliana proteolysis 1 protein (PRT1) and similar proteins; PRT1, also called RING-type E3 ubiquitin transferase PRT1, is an E3 ubiquitin-protein ligase that mediates ubiquitination and subsequent proteasomal degradation of target proteins. It functions in the N-end rule pathway of protein degradation, where it specifically recognizes and ubiquitinates proteins with an N-terminal bulky aromatic amino acid (Phe). It does not act on aliphatic hydrophobic and basic N-terminal residues (Arg or Leu) containing proteins. PRT1 contains a typical C3HC4-type RING-HC finger.


Pssm-ID: 438494 [Multi-domain]  Cd Length: 52  Bit Score: 44.33  E-value: 4.62e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 124430766 730 QSFMCVCCQELVYQPVTTECFHNVCKDCLQRSFKA-QVFSCPACRHDLG 777
Cdd:cd23132    1 EEFLCCICLDLLYKPVVLECGHVFCFWCVHRCMNGyDESHCPLCRRPYD 49
RING-HC_TRIM39_C-IV cd16601
RING finger, HC subclass, found in tripartite motif-containing protein 39 (TRIM39) and similar ...
732-772 5.34e-06

RING finger, HC subclass, found in tripartite motif-containing protein 39 (TRIM39) and similar proteins; TRIM39, also known as RING finger protein 23 (RNF23) or testis-abundant finger protein, is an E3 ubiquitin-protein ligase that plays a role in controlling DNA damage-induced apoptosis through inhibition of the anaphase promoting complex (APC/C), a multiprotein ubiquitin ligase that controls multiple cell cycle regulators, including cyclins, geminin, and others. TRIM39 also functions as a regulator of several key processes in the proliferative cycle. It directly regulates p53 stability. It modulates cell cycle progression and DNA damage responses via stabilizing p21. Moreover, TRIM39 negatively regulates the nuclear factor kappaB (NFkappaB)-mediated signaling pathway through stabilization of Cactin, an inhibitor of NFkappaB- and Toll-like receptor (TLR)-mediated transcription, which is induced by inflammatory stimulants such as tumor necrosis factor alpha. Furthermore, TRIM39 is a MOAP-1-binding protein that can promote apoptosis signaling through stabilization of MOAP-1 via the inhibition of its poly-ubiquitination process. TRIM39 belongs to the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain.


Pssm-ID: 438263 [Multi-domain]  Cd Length: 44  Bit Score: 44.01  E-value: 5.34e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 124430766 732 FMCVCCQELVYQPVTTECFHNVCKDCLQRSFK--AQVFSCPAC 772
Cdd:cd16601    2 ASCSLCKEYLKDPVIIECGHNFCRACITRFWEelDGDFPCPQC 44
RING-HC_RNF169 cd16551
RING finger, HC subclass, found in RING finger protein 169 (RNF169) and similar proteins; ...
731-773 7.47e-06

RING finger, HC subclass, found in RING finger protein 169 (RNF169) and similar proteins; RNF169 is an uncharacterized E3 ubiquitin-protein ligase paralogous to RNF168. It functions as a negative regulator of the DNA damage signaling cascade. RNF169 recognizes polyubiquitin structures but does not itself contribute to double-strand break (DSB)-induced chromatin ubiquitylation. It contributes to regulation of the DSB repair pathway utilization via functionally competing with recruiting repair factors, 53BP1 and RAP80-BRCA1, for association with RNF168-modified chromatin independent of its catalytic activity, limiting the magnitude of the RNF8/RNF168-dependent signaling response to DSBs. RNF169 contains an N-terminal C3HC4-type RING-HC finger and a C-terminal MIU (motif interacting with ubiquitin) domain.


Pssm-ID: 438213 [Multi-domain]  Cd Length: 55  Bit Score: 43.69  E-value: 7.47e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 124430766 731 SFMCVCCQELVYQPVTTECFHNVCKDCLQRSFKAQVF--SCPACR 773
Cdd:cd16551    1 ELTCAGCLEVPVEPATLPCGHTLCRGCANRALDAAEAgpTCPRCR 45
RING-HC_TRIM21_C-IV cd16596
RING finger, HC subclass, found in tripartite motif-containing protein TRIM21 and similar ...
725-779 9.37e-06

RING finger, HC subclass, found in tripartite motif-containing protein TRIM21 and similar proteins; TRIM21, also known as 52 kDa Ro protein, 52 kDa ribonucleoprotein autoantigen Ro/SS-A, Ro(SS-A), RING finger protein 81 (RNF81), or Sjoegren syndrome type A antigen (SS-A), is a ubiquitously expressed E3 ubiquitin-protein ligase and a high affinity antibody receptor uniquely expressed in the cytosol of mammalian cells. As a cytosolic Fc receptor, TRIM21 binds the Fc of virus-associated antibodies and targets the complex in the cytosol for proteasomal degradation in a process known as antibody-dependent intracellular neutralization (ADIN), and provides an intracellular immune response to protect host defense against pathogen infection. It shows remarkably broad isotype specificity as it does not only bind IgG, but also IgM and IgA. Moreover, TRIM21 promotes the cytosolic DNA sensor cGAS and the cytosolic RNA sensor RIG-I sensing of viral genomes during infection by antibody-opsonized virus. It stimulates inflammatory signaling and activates innate transcription factors, such as nuclear factor-kappaB (NF-kappaB). TRIM21 also plays an essential role in p62-regulated redox homeostasis, suggesting it may be a viable target for treating pathological conditions resulting from oxidative damage. Furthermore, TRIM21 may have implications for various autoimmune diseases associated with uncontrolled antiviral signaling through the regulation of Nmi-IFI35 complex-mediated inhibition of innate antiviral response. TRIM21 belongs to the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain.


Pssm-ID: 438258 [Multi-domain]  Cd Length: 77  Bit Score: 44.12  E-value: 9.37e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 124430766 725 LKKLEQSFMCVCCQELVYQPVTTECFHNVCKDCLQRSFKAQVFSCPAC-RHDLGQN 779
Cdd:cd16596    3 LTMMWEEVTCPICLDPFVEPVSIECGHSFCQECISQVGKGGGSVCPVCrQRFLLKN 58
PHD2_PHF10 cd15529
PHD finger 2 found in PHD finger protein 10 (PHF10) and similar proteins; PHF10, also termed ...
348-393 1.01e-05

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: 43.06  E-value: 1.01e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 124430766 348 CHKCGEKRDPNMQLLCDECNMAYHIYCLSppLDKVPEEEyWYCPSC 393
Cdd:cd15529    2 CTKCGDPHDEDKMMFCDQCDRGYHTFCVG--LRSIPDGR-WICPLC 44
PHD1_PHF12 cd15533
PHD finger 1 found in PHD finger protein 12 (PHF12); PHF12, also termed PHD factor 1 (Pf1), is ...
347-393 1.12e-05

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: 43.11  E-value: 1.12e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 124430766 347 SCHKCGEKRDpnmQLLCDECNMAYHIYCLSPPLD--KVPEEEyWYCPSC 393
Cdd:cd15533    1 YCDSCGEGGD---LLCCDRCPASFHLQCCNPPLDeeDLPPGE-WLCHRC 45
RING-HC_TRIM7-like_C-IV cd16594
RING finger, HC subclass, found in tripartite motif-containing proteins, TRIM7, TRIM11 and ...
734-773 1.17e-05

RING finger, HC subclass, found in tripartite motif-containing proteins, TRIM7, TRIM11 and TRIM27, and similar proteins; TRIM7, TRIM11 and TRIM27, closely related tripartite motif-containing proteins, belong to the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox2, and a coiled coil region, as well as a SPRY/B30.2 domain positioned C-terminal to the RBCC domain. TRIM7, also known as glycogenin-interacting protein (GNIP) or RING finger protein 90 (RNF90), is an E3 ubiquitin-protein ligase that mediates c-Jun/AP-1 activation by Ras signalling. Its phosphorylation and activation by MSK1 in response to direct activation by the Ras-Raf-MEK-ERK pathway can stimulate TRIM7 E3 ubiquitin ligase activity in mediating Lys63-linked ubiquitination of the AP-1 coactivator RACO-1, leading to RACO-1 protein stabilization. Moreover, TRIM7 binds and activates glycogenin, the self-glucosylating initiator of glycogen biosynthesis. TRIM11, also known as protein BIA1, or RING finger protein 92 (RNF92), is an E3 ubiquitin-protein ligase involved in the development of the central nervous system. It is overexpressed in high-grade gliomas and promotes proliferation, invasion, migration and glial tumor growth. TRIM11 acts as a potential therapeutic target for congenital central hypoventilation syndrome (CCHS) by mediating the degradation of CCHS-associated polyalanine-expanded Phox2b. TRIM11 modulates the function of neurogenic transcription factor Pax6 through the ubiquitin-proteosome system, and thus plays an essential role for Pax6-dependent neurogenesis. It also binds to and destabilizes a key component of the activator-mediated cofactor complex (ARC105), humanin, a neuroprotective peptide against Alzheimer's disease-relevant insults, and further regulates ARC105 function in transforming growth factor beta (TGFbeta) signaling. Moreover, TRIM11 negatively regulates retinoic acid-inducible gene-I (RIG-I)-mediated interferon-beta (IFNbeta) production and antiviral activity by targeting TANK-binding kinase-1 (TBK1). It may contribute to the endogenous restriction of retroviruses in cells. It enhances N-tropic murine leukemia virus (N-MLV) entry by interfering with Ref1 restriction. It also suppresses the early steps of human immunodeficiency virus HIV-1 transduction, resulting in decreased reverse transcripts. TRIM27, also known as RING finger protein 76 (RNF76), RET finger protein (RFP), or zinc finger protein RFP, is a nuclear E3 ubiquitin-protein ligase that is highly expressed in testis and in various tumor cell lines. Expression of TRIM27 is associated with prognosis of colon and endometrial cancers. TRIM27 was first identified as a fusion partner of the RET receptor tyrosine kinase. It functions as a transcriptional repressor and associates with several proteins involved in transcriptional activity, such as enhancer of polycomb 1 (Epc1), a member of the Polycomb group proteins, and Mi-2beta, a main component of the nucleosome remodeling and deacetylase (NuRD) complex, and the cell cycle regulator retinoblastoma protein (RB1). It also interacts with HDAC1, leading to downregulation of thioredoxin binding protein 2 (TBP-2), which inhibits the function of thioredoxin. Moreover, TRIM27 mediates Pax7-induced ubiquitination of MyoD in skeletal muscle atrophy. In addition, it inhibits muscle differentiation by modulating serum response factor (SRF) and Epc1. TRIM27 promotes a non-canonical polyubiquitination of PTEN, a lipid phosphatase that catalyzes PtdIns(3,4,5)P3 (PIP3) to PtdIns(4,5)P2 (PIP2). It is an IKKepsilon-interacting protein that regulates IkappaB kinase (IKK) function and negatively regulates signaling involved in the antiviral response and inflammation. TRIM27 also forms a protein complex with MBD4 or MBD2 or MBD3, and thus plays an important role in the enhancement of transcriptional repression through MBD proteins in tumorigenesis, spermatogenesis, and embryogenesis. It is a component of an estrogen receptor 1 (ESR1) regulatory complex that is involved in estrogen receptor-mediated transcription in MCF-7 cells.


Pssm-ID: 438256 [Multi-domain]  Cd Length: 61  Bit Score: 43.44  E-value: 1.17e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 124430766 734 CVCCQELVYQPVTTECFHNVCKDCLQRSFKA--QVFSCPACR 773
Cdd:cd16594    8 CPICLDYFTDPVTLDCGHSFCRACIARCWEEpeTSASCPQCR 49
RING-HC_BRCA1 cd16498
RING finger, HC subclass, found in breast cancer type 1 susceptibility protein (BRCA1) and ...
725-773 1.44e-05

RING finger, HC subclass, found in breast cancer type 1 susceptibility protein (BRCA1) and similar proteins; BRCA1, also known as RING finger protein 53 (RNF53), is a RING finger protein encoded by the tumor suppressor gene BRCA1 that regulates all DNA double-strand break (DSB) repair pathways. BRCA1 is frequently mutated in patients with hereditary breast and ovarian cancer (HBOC). Its mutation is also associated with an increased risk of pancreatic, stomach, laryngeal, fallopian tube, and prostate cancer. It plays an important role in the DNA damage response signaling and has been implicated in various cellular processes such as cell cycle regulation, transcriptional regulation, chromatin remodeling, DNA DSBs, and apoptosis. BRCA1 contains an N-terminal C3HC4-type RING-HC finger, and two BRCT (BRCA1 C-terminus domain) repeats at the C-terminus.


Pssm-ID: 438161 [Multi-domain]  Cd Length: 94  Bit Score: 44.21  E-value: 1.44e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 124430766 725 LKKLEQSFMCVCCQELVYQPVTTECFHNVCKDCLQRSF--KAQVFSCPACR 773
Cdd:cd16498   10 ISAMQKNLECPICLELLKEPVSTKCDHQFCRFCILKLLqkKKKPAPCPLCK 60
RING-HC_TRIM38_C-IV cd16600
RING finger, HC subclass, found in tripartite motif-containing protein 38 (TRIM38) and similar ...
727-773 1.91e-05

RING finger, HC subclass, found in tripartite motif-containing protein 38 (TRIM38) and similar proteins; TRIM38, also known as RING finger protein 15 (RNF15) or zinc finger protein RoRet, is an E3 ubiquitin-protein ligase that promotes K63- and K48-linked ubiquitination of cellular proteins and also catalyzes self-ubiquitination. It negatively regulates Tumor necrosis factor alpha (TNF-alpha)- and interleukin-1beta-triggered Nuclear factor-kappaB (NF-kappaB) activation by mediating lysosomal-dependent degradation of transforming growth factor beta (TGFbeta)-activated kinase 1 (TAK1)-binding protein (TAB)2/3, two critical components of the TAK1 kinase complex. It also inhibits TLR3/4-mediated activation of NF-kappaB and interferon regulatory factor 3 (IRF3) by mediating ubiquitin-proteasomal degradation of TNF receptor-associated factor 6 (Traf6) and NAK-associated protein 1 (Nap1), respectively. Moreover, TRIM38 negatively regulates TLR3-mediated interferon beta (IFN-beta) signaling by targeting ubiquitin-proteasomal degradation of TIR domain-containing adaptor inducing IFN-beta (TRIF). It functions as a valid target for autoantibodies in primary Sjogren's Syndrome. TRIM38 belongs the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, a B-box, and two coiled coil domains, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain.


Pssm-ID: 438262 [Multi-domain]  Cd Length: 58  Bit Score: 42.84  E-value: 1.91e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 124430766 727 KLEQSFMCVCCQELVYQPVTTECFHNVCKDCLQRSFKAQ--------VFSCPACR 773
Cdd:cd16600    1 KMREEATCSICLQLMTEPVSINCGHSYCKRCIVSFLENQsqlepgleTFSCPQCR 55
PHD2_KMT2A cd15590
PHD finger 2 found in histone-lysine N-methyltransferase 2A (KMT2A); KMT2A (also termed ALL-1, ...
348-393 2.57e-05

PHD finger 2 found in histone-lysine N-methyltransferase 2A (KMT2A); KMT2A (also termed ALL-1, CXXC-type zinc finger protein 7, myeloid/lymphoid or mixed-lineage leukemia protein 1 (MLL1), trithorax-like protein (Htrx), or zinc finger protein HRX) is a histone methyltransferase that belongs to the MLL subfamily of H3K4-specific histone lysine methyltransferases (KMT2). It regulates chromatin-mediated transcription through the catalysis of methylation of histone 3 lysine 4 (H3K4), and is frequently rearranged in acute leukemia. KMT2A functions as the catalytic subunit in the MLL1 complex, which also contains WDR5, RbBP5, ASH2L and DPY30 as integral core subunits required for the efficient methylation activity of the complex. The MLL1 complex is highly active and specific for H3K4 methylation. KMT2A contains a CxxC (x for any residue) zinc finger domain, three plant homeodomain (PHD) fingers, a Bromodomain domain, an extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, two FY (phenylalanine tyrosine)-rich domains, and a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain. This model corresponds to the second PHD finger.


Pssm-ID: 277065  Cd Length: 50  Bit Score: 42.32  E-value: 2.57e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 124430766 348 CHKCGEKRDPNMQLL-CDECNMAYHIYCLSP--PLDKVPEEEYWYCPSC 393
Cdd:cd15590    2 CHVCGRQHQATKQLLeCNKCRNSYHPECLGPnyPTKPTKKKRVWICTKC 50
RING-HC_ORTHRUS_rpt2 cd23139
second RING finger, HC subclass, found in Arabidopsis thaliana ORTHRUS and similar proteins; ...
727-777 2.71e-05

second RING finger, HC subclass, found in Arabidopsis thaliana ORTHRUS and similar proteins; This subfamily includes Arabidopsis thaliana ORTHRUS 1-5. They are E3 ubiquitin-protein ligases that may participate in CpG methylation-dependent transcriptional regulation and/or epigenetic transcriptional silencing. ORTHRUS 1 mediates ubiquitination with the E2 ubiquitin-conjugating enzymes UBC11, UBC8 and UBC8 homologs (e.g. UBC10, UBC11, UBC28 and UBC29) but not with UBC27, UBC30, UBC32, UBC34 and UBC36. ORTHRUS 2 and 5 mediate ubiquitination with the E2 ubiquitin-conjugating enzyme UBC11. ORTHRUS 1 and 2 promote methylation-mediated gene silencing leading, for example, to early flowering. They can bind to CpG, CpNpG, and CpNpN DNA motifs, with a strong preference for methylated forms, and with highest affinity for CpG substrates. Members of this subfamily contain two typical C3HC4-type RING-HC fingers. This model corresponds to the second one.


Pssm-ID: 438501 [Multi-domain]  Cd Length: 72  Bit Score: 42.83  E-value: 2.71e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 124430766 727 KLEQSFMCVCCQELVYQPVTTECFHNVCKDCLQ----------------RSFKAQ--VFSCPACRHDLG 777
Cdd:cd23139    1 RLLKEFGCQICKKVLSLPVSTPCGHNFCKACLEakfagiadvrdrgnggRSLRARknVKPCPCCKTDIS 69
Ubl_USP48 cd01795
ubiquitin-like (Ubl) domain found in ubiquitin-specific-processing protease 48 (USP48) and ...
19-71 2.72e-05

ubiquitin-like (Ubl) domain found in ubiquitin-specific-processing protease 48 (USP48) and similar proteins; USP48, also termed USP31, or deubiquitinating enzyme 48, or ubiquitin thioesterase 48, or ubiquitin carboxyl-terminal hydrolase 48, belongs to the ubiquitin specific protease (USP) family that is one of at least seven deubiquitylating enzyme (DUB) families capable of deconjugating ubiquitin (Ub)and ubiquitin-like (Ubl) adducts. While the USP proteins have a conserved catalytic core domain, USP48 differs in its domain architecture. It contains an N-terminal USP domain, three DUSP (domain present in ubiquitin-specific protease) domains, and a C-terminal Ubl domain with a beta-grasp Ubl fold, a common structure involved in protein-protein interactions. USP48 is a deubiquitinating enzyme that interacts with TNF receptor-associated factor 2 (TRAF2) and has been implicated in activation of nuclear factor-kappaB (NF-kappaB). Moreover, as a nuclear deubiquitinase regulated by casein kinase 2 (CK2), USP48 controls the ubiquitin/proteasome-system (UPS)-dependent turnover of activated NF-kappaB/RelA in the nucleus together with the COP9 signalosome, suggesting a role of USP48 in a timely control of immune responses.


Pssm-ID: 340493 [Multi-domain]  Cd Length: 99  Bit Score: 43.43  E-value: 2.72e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 124430766  19 VSRKATIEELRERVWALFDVRPECQRLFYRGKQL-ENGYTLFDYDVGLNDIIQL 71
Cdd:cd01795   12 VSSTTTLKELKLQIMEKFSVAPFDQHLYFNGRELtDDSATLADLGILPGDVLYL 65
RING-HC_TRIM5-like_C-IV cd16591
RING finger, HC subclass, found in tripartite motif-containing proteins TRIM5, TRIM6, TRIM22, ...
734-773 2.82e-05

RING finger, HC subclass, found in tripartite motif-containing proteins TRIM5, TRIM6, TRIM22, TRIM34 and similar proteins; TRIM5, TRIM6, TRIM22, and TRIM34, four closely related tripartite motif-containing proteins, belong to the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain. TRIM5, also known as RING finger protein 88 (RNF88), is a capsid-specific restriction factor that prevents infection from non-host-adapted retroviruses in a species-specific manner by binding to and destabilizing the retroviral capsid lattice before reverse transcription is completed. Its retroviral restriction activity correlates with the ability to activate TAK1-dependent innate immune signaling. TRIM5 also acts as a pattern recognition receptor that activates innate immune signaling in response to the retroviral capsid lattice. Moreover, TRIM5 plays a role in regulating autophagy through activation of autophagy regulator BECN1 by causing its dissociation from its inhibitors BCL2 and TAB2. It also plays a role in autophagy by acting as a selective autophagy receptor which recognizes and targets HIV-1 capsid protein p24 for autophagic destruction. TRIM6, also known as RING finger protein 89 (RNF89), is an E3-ubiquitin ligase that cooperates with the E2-ubiquitin conjugase UbE2K to catalyze the synthesis of unanchored K48-linked polyubiquitin chains, and further stimulates the interferon-I kappa B kinase epsilon (IKKepsilon) kinase-mediated antiviral response. It also regulates the transcriptional activity of Myc during the maintenance of embryonic stem (ES) cell pluripotency, and may act as a novel regulator for Myc-mediated transcription in ES cells. TRIM22, also known as 50 kDa-stimulated trans-acting factor (Staf-50) or RING finger protein 94 (RNF94), is an E3 ubiquitin-protein ligase that plays an integral role in the host innate immune response to viruses. It has been shown to inhibit the replication of a number of viruses, including HIV-1, hepatitis B, and influenza A. TRIM22 acts as a suppressor of basal HIV-1 long terminal repeat (LTR)-driven transcription by preventing the transcription factor specificity protein 1 (Sp1) binding to the HIV-1 promoter. It also controls FoxO4 activity and cell survival by directing Toll-like receptor 3 (TLR3)-stimulated cells toward type I interferon (IFN) type I gene induction or apoptosis. Moreover, TRIM22 can activate the noncanonical nuclear factor-kappaB (NF-kappaB) pathway by activating I kappa B kinase alpha (IKKalpha). It also regulates nucleotide binding oligomerization domain containing 2 (NOD2)-dependent activation of interferon-beta signaling and nuclear factor-kappaB. TRIM34, also known as interferon-responsive finger protein 1 or RING finger protein 21 (RNF21), may function as antiviral protein that contribute to the defense against retroviral infections.


Pssm-ID: 438253 [Multi-domain]  Cd Length: 72  Bit Score: 42.81  E-value: 2.82e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 124430766 734 CVCCQELVYQPVTTECFHNVCKDCLQRSFKAQVF-----SCPACR 773
Cdd:cd16591    9 CPICLELLTEPLSLDCGHSFCQACITANHKESVNqegesSCPVCR 53
RING-HC_TRIM47-like_C-IV cd16604
RING finger, HC subclass, found in tripartite motif-containing protein 47 (TRIM47) and similar ...
732-773 3.12e-05

RING finger, HC subclass, found in tripartite motif-containing protein 47 (TRIM47) and similar proteins; TRIM47, also known as gene overexpressed in astrocytoma protein (GOA) or RING finger protein 100 (RNF100), belongs to the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, a B-box, and two coiled coil domains, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain. It plays an important role in the process of dedifferentiation that is associated with astrocytoma tumorigenesis. This subfamily also includes RING finger protein 135 (RNF135). RNF135, also known as RIG-I E3 ubiquitin ligase (REUL) or Riplet, is a widely expressed E3 ubiquitin-protein ligase that consists of an N-terminal C3HC4-type RING-HC finger and C-terminal B30.2/SPRY and PRY motifs, but lacks the B-box and coiled-coil domains that are also typically present in TRIM proteins. RNF135 serves as a specific retinoic acid-inducible gene-I (RIG-I)-interacting protein that ubiquitinates RIG-I and specifically stimulates RIG-I-mediated innate antiviral activity to produce antiviral type-I interferon (IFN) during the early phase of viral infection. It also has been identified as a bio-marker and therapy target of glioblastoma. It associates with the ERK signal transduction pathway and plays a role in glioblastoma cell proliferation, migration and cell cycle.


Pssm-ID: 438266 [Multi-domain]  Cd Length: 49  Bit Score: 42.02  E-value: 3.12e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 124430766 732 FMCVCCQELVYQPVTTECFHNVCKDCLQR---SFKAQVFSCPACR 773
Cdd:cd16604    1 LSCPICLDLLKDPVTLPCGHSFCMGCLGAlwgAGRGGRASCPLCR 45
PHD2_KMT2C_like cd15510
PHD finger 2 found in Histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); KMT2C, ...
348-393 3.17e-05

PHD finger 2 found in Histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3) or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named MLL4, a fourth human homolog of Drosophila trithorax, located on chromosome 12. It enzymatically generates trimethylated histone H3 Lysine 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. KMT2D is also a part of ASCOM. Both KMT2C and KMT2D contain the catalytic domain SET, five plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, a RING finger, an HMG (high-mobilitygroup)-binding motif, and two FY-rich regions. This model corresponds to the second PHD finger.


Pssm-ID: 276985  Cd Length: 46  Bit Score: 41.65  E-value: 3.17e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 124430766 348 CHKCGEKRDPNMQLLCDECNMAYHIYCLSPPLDKVPEEEyWYCPSC 393
Cdd:cd15510    2 CQACRQPGDDTKMLVCETCDKGYHTSCLRPVMSSIPKYG-WKCKNC 46
PHD_BAZ2B cd15630
PHD finger found in bromodomain adjacent to zinc finger domain protein 2B (BAZ2B); BAZ2B, also ...
348-393 3.50e-05

PHD finger found in bromodomain adjacent to zinc finger domain protein 2B (BAZ2B); BAZ2B, also termed WALp4, is a bromodomain-containing protein whose biological role is still elusive. It shows high sequence similarly with BAZ2A, which is the large subunit of the SNF2h-containing chromatin-remodeling complex NoRC that induces nucleosome sliding in an ATP-and histone H4 tail-dependent fashion. BAZ2B contains a TAM (TIP5/ARBP/MBD) domain, an Apolipophorin-III like domain, a DDT domain, four AT-hooks, BAZ 1 and BAZ 2 motifs, a WAKZ (WSTF/Acf1/KIAA0314/ZK783.4) motif, a plant homeodomain (PHD) finger, and a bromodomain.


Pssm-ID: 277100  Cd Length: 49  Bit Score: 41.88  E-value: 3.50e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 124430766 348 CHKCGEKRDPNMQLLCDECNMAYHIYCLSPPLDKVPEEEyWYCPSC 393
Cdd:cd15630    3 CQICRKGDNEELLLLCDGCDKGCHTYCHRPKITTIPEGD-WFCPAC 47
RING-HC_TRIM46_C-I cd16757
RING finger, HC subclass, found in tripartite motif-containing protein 46 (TRIM46) and similar ...
728-773 3.78e-05

RING finger, HC subclass, found in tripartite motif-containing protein 46 (TRIM46) and similar proteins; TRIM46, also known as gene Y protein (GeneY) or tripartite, fibronectin type-III and C-terminal SPRY motif protein (TRIFIC), is a microtubule-associated protein that specifically localizes to the proximal axon, partly overlaps with the axon initial segment (AIS) at later stages, and organizes uniform microtubule orientation in axons. It controls neuronal polarity and axon specification by driving the formation of parallel microtubule arrays. TRIM46 belongs to the C-I subclass of the TRIM (tripartite motif) family of proteins, which are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox2, and a coiled coil region, as well as a COS (carboxyl-terminal subgroup one signature) box, a fibronectin type III (FN3) domain, a PRY domain and a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain.


Pssm-ID: 438415 [Multi-domain]  Cd Length: 43  Bit Score: 41.34  E-value: 3.78e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 124430766 728 LEQSFMCVCCQELVYQPVTTECFHNVCKDCLQRSfkaqVFSCPACR 773
Cdd:cd16757    1 MERELLCPVCKEMYKQPLVLPCMHNVCQVCASEV----LFPCPPCQ 42
RING-HC_TRIM65_C-IV cd16609
RING finger, HC subclass, found in tripartite motif-containing protein TRIM65 and similar ...
729-773 3.81e-05

RING finger, HC subclass, found in tripartite motif-containing protein TRIM65 and similar proteins; TRIM65 is an E3 ubiquitin-protein ligase that interacts with the innate immune receptor MDA5, enhancing its ability to stimulate interferon-beta signaling. It functions as a potential oncogenic protein that negatively regulates p53 through ubiquitination, providing insight into the development of novel approaches targeting TRIM65 for non-small cell lung carcinoma (NSCLC) treatment, and also overcoming chemotherapy resistance. Moreover, TRIM65 negatively regulates microRNA-driven suppression of mRNA translation by targeting TNRC6 proteins for ubiquitination and degradation. TRIM65 belongs to the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain.


Pssm-ID: 438271 [Multi-domain]  Cd Length: 58  Bit Score: 41.97  E-value: 3.81e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 124430766 729 EQSFMCVCCQELVYQPVTTECFHNVCKDCLQRSFK---AQVFSCPACR 773
Cdd:cd16609    1 EEELTCSICLGLYQDPVTLPCQHSFCRACIEDHWRqkdEGSFSCPECR 48
RING-HC_CHFR cd16503
RING finger, HC subclass, found in checkpoint with forkhead and RING finger domains protein ...
734-773 3.99e-05

RING finger, HC subclass, found in checkpoint with forkhead and RING finger domains protein (CHFR); CHFR, also known as RING finger protein 196 (RNF196), is a checkpoint protein that delays entry into mitosis in response to stress. It functions as an E3 ubiquitin ligase that ubiquitinates and degrades its target proteins, such as Aurora-A, Plk1, Kif22, and PARP-1, which are critical for proper mitotic transitions. It also plays an important role in cell cycle progression and tumor suppression, and is negatively regulated by SUMOylation-mediated proteasomal ubiquitylation. Moreover, CHFR is involved in the early stage of the DNA damage response, which mediates the crosstalk between ubiquitination and poly-ADP-ribosylation. CHFR contains a fork head associated (FHA) domain and a C3HC4-type RING-HC finger.


Pssm-ID: 438166 [Multi-domain]  Cd Length: 55  Bit Score: 41.58  E-value: 3.99e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 124430766 734 CVCCQELVYQPVTTE-CFHNVCKDCLQRSFKAQVFSCPACR 773
Cdd:cd16503    5 CSICQDLLHDCVSLQpCMHNFCAACYSDWMERSNTECPTCR 45
RING-HC_TRY3-like cd23137
RING finger, HC subclass, found in Candida albicans transcriptional regulator of yeast form ...
732-774 4.48e-05

RING finger, HC subclass, found in Candida albicans transcriptional regulator of yeast form adherence 3 (TRY3) and similar proteins; TRY3 acts as a transcription factor required for yeast cell adherence to silicone substrate. It contains a typical C3HC4-type RING-HC finger.


Pssm-ID: 438499 [Multi-domain]  Cd Length: 53  Bit Score: 41.68  E-value: 4.48e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 124430766 732 FMCVCCQELVYQPVTTECFHNVCKDCLQRSFKAQVFSCPACRH 774
Cdd:cd23137    3 YACPICMNVAWKPVRLECSHVFCLRCLVKAQKQKKDNCPLCRA 45
PHD_PHF21B cd15524
PHD finger found in PHD finger protein 21B (PHF21B); PHF21B is a plant homeodomain (PHD) ...
348-393 4.57e-05

PHD finger found in PHD finger protein 21B (PHF21B); PHF21B is a plant homeodomain (PHD) finger-containing protein whose biological function remains unclear. It shows high sequence similarity with PHF21A, which is associated with LSD1, a lysine (K)-specific histone demethylase and inhibits LSD1-mediated histone demethylation in vitro. PHD fingers can recognize the unmodified and modified histone H3 tail, and some have been found to interact with non-histone proteins.


Pssm-ID: 276999 [Multi-domain]  Cd Length: 43  Bit Score: 41.42  E-value: 4.57e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 124430766 348 CHKCgeKRDPNMQLlCDECNMAYHIYCLSPPLdKVPEEEYWYCPSC 393
Cdd:cd15524    2 CAAC--KRGGNLQP-CGTCPRAYHLDCLDPPL-KTAPKGVWVCPKC 43
RING-HC_RNF114 cd16540
RING finger, HC subclass, found in RING finger protein 114 (RNF114) and similar proteins; ...
732-776 4.64e-05

RING finger, HC subclass, found in RING finger protein 114 (RNF114) and similar proteins; RNF114, also known as zinc finger protein 228 (ZNF228) or zinc finger protein 313 (ZNF313), is a p21(WAF1)-targeting ubiquitin E3 ligase that interacts with X-linked inhibitor of apoptosis (XIAP)-associated factor 1 (XAF1) and may play a role in p53-mediated cell-fate decisions. It is involved in the immune response to double-stranded RNA in disease pathogenesis. Moreover, RNF114 interacts with A20 and modulates its ubiquitylation. It negatively regulates nuclear factor-kappaB (NF-kappaB)-dependent transcription and positively regulates T-cell activation. RNF114 may play a putative role in the regulation of immune responses, since it corresponds to a novel psoriasis susceptibility gene, ZNF313. RNF114, together with three closely related proteins: RNF125, RNF138 and RNF166, forms a novel family of ubiquitin ligases with a C3HC4-type RING-HC finger, a C2HC-, and two C2H2-type zinc fingers, as well as a ubiquitin interacting motif (UIM).


Pssm-ID: 438202 [Multi-domain]  Cd Length: 46  Bit Score: 41.28  E-value: 4.64e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 124430766 732 FMCVCCQELVYQPVTTECFHNVCKDCLQRSFKAQVFSCPACRHDL 776
Cdd:cd16540    2 FTCPVCLEIFETPVRVPCGHVFCNACLQECLKPKKPVCAVCRSPL 46
zf-C3HC4 pfam00097
Zinc finger, C3HC4 type (RING finger); The C3HC4 type zinc-finger (RING finger) is a ...
734-772 4.87e-05

Zinc finger, C3HC4 type (RING finger); The C3HC4 type zinc-finger (RING finger) is a cysteine-rich domain of 40 to 60 residues that coordinates two zinc ions, and has the consensus sequence: C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C where X is any amino acid. Many proteins containing a RING finger play a key role in the ubiquitination pathway.


Pssm-ID: 395049 [Multi-domain]  Cd Length: 40  Bit Score: 41.19  E-value: 4.87e-05
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 124430766  734 CVCCQELVYQPVTTECFHNVCKDCLQRSFKAQVFSCPAC 772
Cdd:pfam00097   2 PICLEEPKDPVTLLPCGHLFCSKCIRSWLESGNVTCPLC 40
rad18 TIGR00599
DNA repair protein rad18; All proteins in this family for which functions are known are ...
725-773 5.40e-05

DNA repair protein rad18; All proteins in this family for which functions are known are involved in nucleotide excision repair.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273165 [Multi-domain]  Cd Length: 397  Bit Score: 46.15  E-value: 5.40e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 124430766  725 LKKLEQSFMCVCCQELVYQPVTTECFHNVCKDCLQRSFKAQVfSCPACR 773
Cdd:TIGR00599  20 LYPLDTSLRCHICKDFFDVPVLTSCSHTFCSLCIRRCLSNQP-KCPLCR 67
RAD18 COG5432
RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms];
725-775 6.31e-05

RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms];


Pssm-ID: 227719 [Multi-domain]  Cd Length: 391  Bit Score: 46.23  E-value: 6.31e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 124430766 725 LKKLEQSFMCVCCQELVYQPVTTECFHNVCKDCLQRSFKAQVFsCPACRHD 775
Cdd:COG5432   19 LKGLDSMLRCRICDCRISIPCETTCGHTFCSLCIRRHLGTQPF-CPVCRED 68
RING-HC_TRIM69_C-IV cd16611
RING finger, HC subclass, found in tripartite motif-containing protein 69 (TRIM69) and similar ...
728-773 6.61e-05

RING finger, HC subclass, found in tripartite motif-containing protein 69 (TRIM69) and similar proteins; TRIM69, also known as RFP-like domain-containing protein trimless or RING finger protein 36 (RNF36), is a testis E3 ubiquitin-protein ligase that plays a specific role in apoptosis and may also play an important role in germ cell homeostasis during spermatogenesis. TRIM69 belongs to the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain.


Pssm-ID: 438273 [Multi-domain]  Cd Length: 59  Bit Score: 41.28  E-value: 6.61e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 124430766 728 LEQSFMCVCCQELVYQPVTTECFHNVCKDCLQRSFKAQV--FSCPACR 773
Cdd:cd16611    1 LTEELHCPLCLDFFRDPVMLSCGHNFCQSCITGFWELQAedTTCPECR 48
RING-HC_LONFs_rpt1 cd16513
first RING finger, HC subclass, found in the LON peptidase N-terminal domain and RING finger ...
732-777 8.51e-05

first RING finger, HC subclass, found in the LON peptidase N-terminal domain and RING finger protein family; The LON peptidase N-terminal domain and RING finger protein family includes LONRF1 (also known as RING finger protein 191 or RNF191), LONRF2 (also known as RING finger protein 192, RNF192, or neuroblastoma apoptosis-related protease), LONRF3 (also known as RING finger protein 127 or RNF127), which are characterized by containing two C3HC4-type RING-HC fingers, four tetratricopeptide (TPR) repeats, and an ATP-dependent protease La (LON) substrate-binding domain at the C-terminus. Their biological functions remain unclear. This model corresponds to the first RING-HC finger.


Pssm-ID: 438176 [Multi-domain]  Cd Length: 47  Bit Score: 40.37  E-value: 8.51e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 124430766 732 FMCVCCQELVYQPVTTECFHNVCKDCLQRSFKAQvfsCPACRHDLG 777
Cdd:cd16513    3 LSCPLCRGLLFEPVTLPCGHTFCKRCLERDPSSR---CRLCRLKLS 45
RING-HC_RNF151 cd16547
RING finger, HC subclass, found in RING finger protein 151 (RNF151) and similar proteins; ...
729-778 8.53e-05

RING finger, HC subclass, found in RING finger protein 151 (RNF151) and similar proteins; RNF151 is a testis-specific RING finger protein that interacts with dysbindin, a synaptic and microtubular protein that binds brain snapin, a SNARE-binding protein that mediates intracellular membrane fusion in both neuronal and non-neuronal cells. Thus, it may be involved in acrosome formation of spermatids by interacting with multiple proteins participating in membrane biogenesis and microtubule organization. RNF151 contains a C3HC4-type RING finger domain, a putative nuclear localization signal (NLS), and a TNF receptor associated factor (TRAF)-type zinc finger domain.


Pssm-ID: 438209 [Multi-domain]  Cd Length: 49  Bit Score: 40.52  E-value: 8.53e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 124430766 729 EQSFMCVCCQELVYQPVTTECFHNVCKDCLQRSFKAQVfSCPACRHDLGQ 778
Cdd:cd16547    1 DDDLICSICHGVLRCPVRLSCSHIFCKKCILQWLKRQE-TCPCCRKEVKG 49
RING-HC_TRIM17_C-IV cd16595
RING finger, HC subclass, found in tripartite motif-containing protein TRIM17 and similar ...
727-773 1.03e-04

RING finger, HC subclass, found in tripartite motif-containing protein TRIM17 and similar proteins; TRIM17, also known as RING finger protein 16 (RNF16) or testis RING finger protein (Terf), is a crucial E3 ubiquitin ligase that is necessary and sufficient for neuronal apoptosis and contributes to Mcl-1 ubiquitination in cerebellar granule neurons (CGNs). It interacts in a SUMO-dependent manner with nuclear factor of activated T cell NFATc3 transcription factor, and thus inhibits the activity of NFATc3 by preventing its nuclear localization. In contrast, it binds to and inhibits NFATc4 transcription factor in a SUMO-independent manner. Moreover, TRIM17 stimulates degradation of kinetochore protein ZW10 interacting protein (ZWINT), a known component of the kinetochore complex required for the mitotic spindle checkpoint, and negatively regulates cell proliferation. TRIM17 belongs to the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain.


Pssm-ID: 438257 [Multi-domain]  Cd Length: 70  Bit Score: 41.13  E-value: 1.03e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 124430766 727 KLEQSFMCVCCQELVYQPVTTECFHNVCKDCLQRSFK-----------AQVFSCPACR 773
Cdd:cd16595    1 RLQEEATCSICLDYFTDPVMTTCGHNFCRACIQLSWEkargkkgrrkqKGSFPCPECR 58
RING-HC_MID2 cd16754
RING finger, HC subclass, found in midline-2 (MID2) and similar proteins; MID2, also known as ...
725-786 1.21e-04

RING finger, HC subclass, found in midline-2 (MID2) and similar proteins; MID2, also known as midin-2, midline defect 2, RING finger protein 60 (RNF60), or tripartite motif-containing protein 1 (TRIM1), is a probable E3 ubiquitin-protein ligase and is highly related to MID1 that associates with cytoplasmic microtubules along their length and throughout the cell cycle. Like MID1, MID2 associates with the microtubule network and may at least partially compensate for the loss of MID1. Both MID1 and MID2 interacts with Alpha 4, which is a regulatory subunit of PP2-type phosphatases, such as PP2A, and an integral component of the rapamycin-sensitive signaling pathway. MID2 can also substitute for MID1 to control exocytosis of lytic granules in cytotoxic T cells. Loss-of-function mutations in MID2 lead to the human X-linked intellectual disability (XLID). MID2 belongs to the C-I subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a COS (carboxy-terminal subgroup one signature) box, a fibronectin type III (FN3) domain, and a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain. MID2 hetero-dimerizes in vitro with its paralog MID1.


Pssm-ID: 438412 [Multi-domain]  Cd Length: 70  Bit Score: 40.74  E-value: 1.21e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 124430766 725 LKKLEQSFMCVCCQELVYQPVTTECFHNVCKDCLQRSFKAQ-----------VFSCPACRhdlgqnYVMVLNE 786
Cdd:cd16754    1 METLESELTCPICLELFEDPLLLPCAHSLCFSCAHRILTSGcasgesieppsAFQCPTCR------YVISLNH 67
RING-HC_MmTRIM43-like cd23133
RING finger, HC subclass, found in Mus musculus tripartite motif-containing protein 43 (TRIM43) ...
729-781 1.28e-04

RING finger, HC subclass, found in Mus musculus tripartite motif-containing protein 43 (TRIM43) and similar propteins; This subfamily includes TRIM43A, TRIM43B and TRIM43C, which are expressed specifically in mouse preimplantation embryos. They contain a typical C3HC4-type RING-HC finger.


Pssm-ID: 438495 [Multi-domain]  Cd Length: 57  Bit Score: 40.28  E-value: 1.28e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 124430766 729 EQSFMCVCCQELVYQPVTTECFHNVCKDCLQRSFKAQVFS--CPACRHDLGQNYV 781
Cdd:cd23133    1 EETLTCSICQGIFMNPVYLRCGHKFCEACLLLFQEDIKFPayCPMCRQPFNQEYI 55
PHD2_KMT2A_like cd15507
PHD finger 2 found in histone-lysine N-methyltransferase 2A (KMT2A) and 2B (KMT2B); This ...
347-393 1.52e-04

PHD finger 2 found in histone-lysine N-methyltransferase 2A (KMT2A) and 2B (KMT2B); This family includes histone-lysine N-methyltransferase trithorax (Trx) like proteins, KMT2A (MLL1) and KMT2B (MLL2), which comprise the mammalian Trx branch of the COMPASS family, and are both essential for mammalian embryonic development. KMT2A regulates chromatin-mediated transcription through the catalysis of methylation of histone 3 lysine 4 (H3K4), and is frequently rearranged in acute leukemia. KMT2A functions as the catalytic subunit in the MLL1 complex. KMT2B is a second human homolog of Drosophila trithorax, located on chromosome 19 and functions as the catalytic subunit in the MLL2 complex. It plays a critical role in memory formation through mediating hippocampal H3K4 di- and trimethylation. It is also required for RNA polymerase II association and protection from DNA methylation at the MagohB CpG island promoter. Both KMT2A and KMT2B contain a CxxC (x for any residue) zinc finger domain, three plant homeodomain (PHD) fingers, an extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, two FY (phenylalanine tyrosine)-rich domains, and a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain. This model corresponds to the second PHD finger.


Pssm-ID: 276982  Cd Length: 50  Bit Score: 40.14  E-value: 1.52e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 124430766 347 SCHKCGEKRDPNMQLL-CDECNMAYHIYCLSPPLDKVPE--EEYWYCPSC 393
Cdd:cd15507    1 FCHVCGRKGQAQKQLLeCEKCQRGYHVDCLGPSYPTKPTrkKKTWICSKC 50
RING-HC_RNF39 cd16592
RING finger, HC subclass, found in RING finger protein 39 (RNF39) and similar proteins; RNF39, ...
728-773 1.59e-04

RING finger, HC subclass, found in RING finger protein 39 (RNF39) and similar proteins; RNF39, also called protein HZFw, may play a role in prolonged long term-potentiation (LTP) maintenance. It is involved in the etiology of Behcet's disease (BD). It may also be involved in HIV-1 replication. RNF39 acts as an E3 ubiquitin ligase that inhibits retinoic acid-inducible gene-I (RIG-I)-like receptor (RLR) pathways by mediating K48-linked ubiquitination and proteasomal degradation of DDX3X (DEAD-box RNA helicase 3, X-linked). RNF39 contains a typical C3HC4-type RING-HC finger.


Pssm-ID: 438254 [Multi-domain]  Cd Length: 58  Bit Score: 40.13  E-value: 1.59e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 124430766 728 LEQSFMCVCCQELVYQPVTTECFHNVCKDCLQRSFK--------AQVFSCPACR 773
Cdd:cd16592    1 LQEETTCPICLGYFKDPVILDCEHSFCRACIARHWGqeamegngAEGVFCPQCG 54
PHD_Phf1p_Phf2p_like cd15502
PHD finger found in Schizosaccharomyces pombe SWM histone demethylase complex subunits Phf1 ...
345-393 1.72e-04

PHD finger found in Schizosaccharomyces pombe SWM histone demethylase complex subunits Phf1 (Phf1p) and Phf2 (Phf2p); Phf1p and Phf2p are components of the SWM histone demethylase complex that specifically demethylates histone H3 at lysine 9 (H3K9me2), a specific tag for epigenetic transcriptional activation. They function as corepressors and play roles in regulating heterochromatin propagation and euchromatic transcription. Both Phf1p and Phf2p contain a plant homeodomain (PHD) finger.


Pssm-ID: 276977  Cd Length: 52  Bit Score: 39.73  E-value: 1.72e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 124430766 345 MCSCHKCGEKRDPNMQLLCDECNMAYHIYCLSPPLDKVPEEEY---WYCPSC 393
Cdd:cd15502    1 VCIVCQRGHSPKSNRIVFCDGCNTPYHQLCHDPSIDDEVVEDPdaeWFCKKC 52
RING-HC_dBre1-like cd16705
RING finger, HC subclass, found in Drosophila melanogaster Bre1 (dBre1) and similar proteins; ...
725-779 2.38e-04

RING finger, HC subclass, found in Drosophila melanogaster Bre1 (dBre1) and similar proteins; dBre1 is the functional homolog of yeast Bre1, an E3 ubiquitin ligase required for the monoubiquitination of histone H2B and, indirectly, for H3K4 methylation. dBre1 acts as a nuclear component required for the expression of Notch target genes in Drosophila development. dBre1 contains a C3HC4-type RING-HC finger at its C-terminus.


Pssm-ID: 438365 [Multi-domain]  Cd Length: 69  Bit Score: 39.95  E-value: 2.38e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 124430766 725 LKKLEQSFMCVCCQELVYQPVTTECFHNVCKDCLQRSFKAQVFSCPACRHDLGQN 779
Cdd:cd16705    8 IREYKEQLTCPSCKVKRKDAVLTKCFHVFCLDCLRTRYETRQRKCPKCNAAFGAN 62
RING-HC_MID1 cd16753
RING finger, HC subclass, found in midline-1 (MID1) and similar proteins; MID1, also known as ...
728-786 2.46e-04

RING finger, HC subclass, found in midline-1 (MID1) and similar proteins; MID1, also known as midin, midline 1 RING finger protein, putative transcription factor XPRF, RING finger protein 59 (RNF59), or tripartite motif-containing protein 18 (TRIM18), is a microtubule-associated E3 ubiquitin-protein ligase implicated in epithelial-mesenchymal differentiation, cell migration and adhesion, and programmed cell death along specific regions of the ventral midline during embryogenesis. It monoubiquinates the alpha4 subunit of protein phosphatase 2A (PP2A), promoting proteosomal degradation of the catalytic subunit of PP2A (PP2Ac) and preventing the A and B subunits from forming an active complex. It promotes allergen and rhinovirus-induced asthma through the inhibition of PP2A activity. It is strongly upregulated in cytotoxic lymphocytes (CTLs) and directs lytic granule exocytosis and cytotoxicity of killer T cells. Loss-of-function mutations in MID1 lead to the human X-linked Opitz G/BBB (XLOS) syndrome characterized by defective midline development during embryogenesis. MID1 belongs to the C-I subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a COS (carboxyl-terminal subgroup one signature) box, a fibronectin type III (FN3) domain, and a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain. MID1 hetero-dimerizes in vitro with its paralog MID2.


Pssm-ID: 438411 [Multi-domain]  Cd Length: 72  Bit Score: 40.02  E-value: 2.46e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124430766 728 LEQSFMCVCCQELVYQPVTTECFHNVCKDCLQRSFKAQ-----------VFSCPACRhdlgqnYVMVLNE 786
Cdd:cd16753    2 LESELTCPICLELFEDPLLLPCAHSLCFNCAHRILVSHcasnesvesitAFQCPTCR------YVITLNQ 65
PHD1_Rco1 cd15535
PHD finger 1 found in Saccharomyces cerevisiae transcriptional regulatory protein Rco1 and ...
345-393 2.52e-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: 39.32  E-value: 2.52e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 124430766 345 MCS-CHKCGEkrdpnmQLLCDECNMAYHIYCLSPPLDK--VPEEEyWYCPSC 393
Cdd:cd15535    1 FCSaCGGYGS------FLCCDGCPRSFHFSCLDPPLEEdnLPDDE-WFCNEC 45
RING-HC_RING2 cd16740
RING finger, HC subclass, found in really interesting new gene 2 protein (RING2) and similar ...
726-776 2.54e-04

RING finger, HC subclass, found in really interesting new gene 2 protein (RING2) and similar proteins; RING2, also known as huntingtin-interacting protein 2-interacting protein 3, HIP2-interacting protein 3, protein DinG, RING finger protein 1B (RING1B), RING finger protein 2 (RNF2), or RING finger protein BAP-1, is an E3 ubiquitin-protein ligase that interacts with both nucleosomal DNA and an acidic patch on histone H4 to achieve the specific monoubiquitination of K119 on histone H2A (H2AK119ub), thereby playing a central role in histone code and gene regulation. RING2 is a core component of polycomb repressive complex 1 (PRC1) that functions as an E3-ubuiquitin ligase transferring the mono-ubuiquitin mark to the C-terminal tail of Histone H2A at K118/K119. PRC1 is also capable of chromatin compaction, a function not requiring histone tails, and this activity appears important in gene silencing. The enzymatic activity of RING2 is enhanced by the interaction with BMI1/PCGF4, and it is dispensable for early embryonic development and much of the gene repression activity of PRC1. Moreover, RING2 plays a key role in terminating neural precursor cell (NPC)-mediated production of subcerebral projection neurons (SCPNs) during neocortical development. It also plays a critical role in nonhomologous end-joining (NHEJ)-mediated end-to-end chromosome fusions. Furthermore, RING2 is essential for expansion of hepatic stem/progenitor cells. It promotes hepatic stem/progenitor cell expansion through simultaneous suppression of cyclin-dependent kinase inhibitors (CDKIs) Cdkn1a and Cdkn2a, known negative regulators of cell proliferation. RING2 also negatively regulates p53 expression through directly binding with both p53 and MDM2 and promoting MDM2-mediated p53 ubiquitination in selective cancer cell types to stimulate tumor development. RING2 contains a C3HC4-type RING-HC finger.


Pssm-ID: 438398 [Multi-domain]  Cd Length: 77  Bit Score: 40.07  E-value: 2.54e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 124430766 726 KKLEQSFMCVCCQELVYQPVTT-ECFHNVCKDCLQRSFKAQVFSCPACRHDL 776
Cdd:cd16740    7 RSLHSELMCPICLDMLKNTMTTkECLHRFCADCIITALRSGNKECPTCRKKL 58
RING-HC_RING1 cd16739
RING finger, HC subclass, found in really interesting new gene 1 protein (RING1) and similar ...
732-797 2.74e-04

RING finger, HC subclass, found in really interesting new gene 1 protein (RING1) and similar proteins; RING1, also known as polycomb complex protein RING1, RING finger protein 1 (RNF1), or RING finger protein 1A (RING1A), was identified as a transcriptional repressor that is associated with the Polycomb group (PcG) protein complex involved in stable repression of gene activity. It is a core component of polycomb repressive complex 1 (PRC1) that functions as an E3-ubuiquitin ligase that transferring the mono-ubuiquitin mark to the C-terminal tail of Histone H2A at K118/K119. PRC1 is also capable of chromatin compaction, a function not requiring histone tails, and this activity appears important in gene silencing. RING1 interacts with multiple PcG proteins and displays tumorigenic activity. It also shows zinc-dependent DNA binding activity. Moreover, RING1 inhibits transactivation of the DNA-binding protein recombination signal binding protein-Jkappa (RBP-J) by Notch through interaction with the LIM domains of KyoT2. RING1 contains a C3HC4-type RING-HC finger.


Pssm-ID: 438397 [Multi-domain]  Cd Length: 70  Bit Score: 40.06  E-value: 2.74e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 124430766 732 FMCVCCQELVYQPVTT-ECFHNVCKDCLQRSFKAQVFSCPACRHDLGQNYVMVLNETLQTLLDLFFP 797
Cdd:cd16739    4 LMCPICLDMLKNTMTTkECLHRFCSDCIVTALRSGNKECPTCRKKLVSKRSLRPDPNFDALISKIYP 70
RING-HC_TRIM35_C-IV cd16599
RING finger, HC subclass, found in tripartite motif-containing protein 35 (TRIM35) and similar ...
728-773 2.79e-04

RING finger, HC subclass, found in tripartite motif-containing protein 35 (TRIM35) and similar proteins; TRIM35, also known as hemopoietic lineage switch protein 5 (HLS5), is a putative hepatocellular carcinoma (HCC) suppressor that inhibits phosphorylation of pyruvate kinase isoform M2 (PKM2), which is involved in aerobic glycolysis of cancer cells and further suppresses the Warburg effect and tumorigenicity in HCC. It also negatively regulates Toll-like receptor 7 (TLR7)- and TLR9-mediated type I interferon production by suppressing the stability of interferon regulatory factor 7 (IRF7). Moreover, TRIM35 regulates erythroid differentiation by modulating globin transcription factor 1 (GATA-1) activity. TRIM35 belongs to the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain.


Pssm-ID: 438261 [Multi-domain]  Cd Length: 66  Bit Score: 39.75  E-value: 2.79e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 124430766 728 LEQSFMCVCCQELVYQPVTTECFHNVCKDCLQRSFKAQV-FSCPACR 773
Cdd:cd16599    1 FKEELLCPICYEPFREAVTLRCGHNFCKGCVSRSWERQPrAPCPVCK 47
PHD2_KMT2B cd15591
PHD domain 2 found in Histone-lysine N-methyltransferase 2B (KMT2B); KMT2B, also termed ...
348-393 3.30e-04

PHD domain 2 found in Histone-lysine N-methyltransferase 2B (KMT2B); KMT2B, also termed trithorax homolog 2 or WW domain-binding protein 7 (WBP-7), is encoded by the gene that was first named myeloid/lymphoid or mixed-lineage leukemia 2 (MLL2), a second human homolog of Drosophila trithorax, located on chromosome 19. It belongs to the MLL subfamily of H3K4-specific histone lysine methyltransferases (KMT2) and is vital for normal mammalian embryonic development. KMT2B functions as the catalytic subunit in the MLL2 complex, which contains WDR5, RbBP5, ASH2L and DPY30 as integral core subunits required for the efficient methylation activity of the complex. The MLL2 complex is highly active and specific for histone 3lysine 4 (H3K4) methylation, which stimulates chromatin transcription in a SAM- and H3K4-dependent manner. Moreover, KMT2B plays a critical role in memory formation through mediating hippocampal H3K4 di- and trimethylation. It is also required for RNA polymerase II association and protection from DNA methylation at the MagohB CpG island promoter. KMT2B contains a CxxC (x for any residue) zinc finger domain, three plant homeodomain (PHD), an extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, two FY (phenylalanine tyrosine)-rich domains, and a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain. This model corresponds to the second PHD finger.


Pssm-ID: 277066  Cd Length: 50  Bit Score: 39.15  E-value: 3.30e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 124430766 348 CHKCGEKRDPNMQLL-CDECNMAYHIYCLSP--PLDKVPEEEYWYCPSC 393
Cdd:cd15591    2 CHVCGRKNKESKPLLeCERCRNCYHPACLGPnyPKPANRKKRPWICSAC 50
RING-HC_RAG1 cd16530
RING finger, HC subclass, found in recombination activating gene-1 (RAG-1) and similar ...
730-774 3.80e-04

RING finger, HC subclass, found in recombination activating gene-1 (RAG-1) and similar proteins; RAG-1, also known as V(D)J recombination-activating protein 1, RING finger protein 74 (RNF74), or endonuclease RAG1, is the catalytic component of the RAG complex, a multiprotein complex that mediates the DNA cleavage phase during V(D)J recombination. RAG1 is a lymphoid-specific factor that mediates DNA-binding to conserved recombination signal sequences (RSS) and catalyzes DNA cleavage activities by introducing a double-strand break between the RSS and the adjacent coding segment. It also functions as an E3 ubiquitin-protein ligase that mediates monoubiquitination of histone H3, which is required for the joining step of V(D)J recombination. RAG-1 contains an N-terminal C3HC4-type RING-HC finger that mediates monoubiquitylation of histone H3, an adjacent C2H2-type zinc finger, and a nonamer binding (NBD) DNA-binding domain.


Pssm-ID: 319444 [Multi-domain]  Cd Length: 46  Bit Score: 38.58  E-value: 3.80e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 124430766 730 QSFMCVCCQELVYQPVTTECFHNVCKDCLQRSFKAQVFSCPACRH 774
Cdd:cd16530    1 KSVSCQVCEHILADPVQTPCKHLFCRTCILKCLKVMGSYCPSCRY 45
RING-HC_TRIM9-like_C-I cd16576
RING finger, HC subclass, found in tripartite motif-containing proteins TRIM9, TRIM67, and ...
729-773 3.82e-04

RING finger, HC subclass, found in tripartite motif-containing proteins TRIM9, TRIM67, and similar proteins; Tripartite motif-containing proteins TRIM9 and TRIM67 belong to the C-I subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, consisting of three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a COS (carboxyl-terminal subgroup one signature) box, a fibronectin type III (FN3) domain, and a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain. TRIM9 (the human ortholog of rat Spring), also known as RING finger protein 91 (RNF91), is a brain-specific E3 ubiquitin-protein ligase collaborating with an E2 ubiquitin conjugating enzyme UBCH5b. TRIM9 plays an important role in the regulation of neuronal functions and participates in neurodegenerative disorders through its ligase activity. TRIM67, also known as TRIM9-like protein (TNL), is a protein selectively expressed in the cerebellum. It interacts with PRG-1, an important molecule in the control of hippocampal excitability dependent on presynaptic LPA2 receptor signaling, and 80K-H, also known as glucosidase II beta, a protein kinase C substrate.


Pssm-ID: 438238 [Multi-domain]  Cd Length: 42  Bit Score: 38.55  E-value: 3.82e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 124430766 729 EQSFMCVCCQELVYQPVTTECFHNVCKDCLqrsfKAQVFSCPACR 773
Cdd:cd16576    1 EEELKCPVCGSLFTEPVILPCSHNLCLGCA----LNIQLTCPICH 41
RING-HC_RNF40 cd16815
RING finger, HC subclass, found in RING finger protein 40 (RNF40); RNF40, also known as BRE1B ...
725-779 3.97e-04

RING finger, HC subclass, found in RING finger protein 40 (RNF40); RNF40, also known as BRE1B or 95 kDa retinoblastoma-associated protein (RBP95), was identified as a novel leucine zipper retinoblastoma protein (pRb)-associated protein that may function as a regulation factor in RNA polymerase II-mediated transcription and/or transcriptional processing. RNF40 also functions as an E3 ubiquitin-protein ligase that forms a heterodimeric complex with BRE1B, also known as RNF40, to facilitate the K120 monoubiquitination of histone H2B (H2Bub1), a DNA damage-induced histone modification that is crucial for recruitment of the chromatin remodeler SNF2h to DNA double-strand break (DSB) damage sites. It cooperates with SUPT16H to induce dynamic changes in chromatin structure during DSB repair. RNF40 contains a C3HC4-type RING-HC finger at the C-terminus.


Pssm-ID: 438464 [Multi-domain]  Cd Length: 78  Bit Score: 39.63  E-value: 3.97e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 124430766 725 LKKLEQSFMCVCCQELVYQPVTTECFHNVCKDCLQRSFKAQVFSCPACRHDLGQN 779
Cdd:cd16815   17 IKEYKARLTCPCCNTRKKDAVLTKCFHVFCFECVKTRYESRQRKCPKCNAAFGAH 71
RING-HC_RNF166 cd16549
RING finger, HC subclass, found in RING finger protein 166 (RNF166) and similar proteins; ...
732-773 4.49e-04

RING finger, HC subclass, found in RING finger protein 166 (RNF166) and similar proteins; RNF166 is encoded by the gene RNF166 targeted by thyroid hormone receptor alpha1 (TRalpha1), which is important in brain development. It plays an important role in RNA virus-induced interferon-beta production by enhancing the ubiquitination of TRAF3 and TRAF6. RNF166, together with three closely related proteins: RNF114, RNF125 and RNF138, forms a novel family of ubiquitin ligases with a C3HC4-type RING-HC finger, a C2HC-, and two C2H2-type zinc fingers, as well as a ubiquitin interacting motif (UIM).


Pssm-ID: 438211 [Multi-domain]  Cd Length: 47  Bit Score: 38.64  E-value: 4.49e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 124430766 732 FMCVCCQELVYQPV-TTECFHNVCKDCLQRSFKAQVFSCPACR 773
Cdd:cd16549    2 FSCPICLEVYHKPVvITSCGHTFCGECLQPCLQVASPLCPLCR 44
RING-HC_TRIM77_C-IV cd16543
RING finger, HC subclass, found in tripartite motif-containing protein 77 (TRIM77) and similar ...
729-773 5.77e-04

RING finger, HC subclass, found in tripartite motif-containing protein 77 (TRIM77) and similar proteins; TRIM77 belongs to the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including two consecutive zinc-binding domains, a C3HC4-type RING-HC finger and Bbox2, as well as a SPRY/B30.2 domain positioned C-terminal to the RBCC domain.


Pssm-ID: 438205 [Multi-domain]  Cd Length: 54  Bit Score: 38.53  E-value: 5.77e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 124430766 729 EQSFMCVCCQELVYQPVTTECFHNVCKDCLQRSF--KAQVFSCPACR 773
Cdd:cd16543    1 EDQLTCSICLDLLKDPVTIPCGHSFCMNCITLLWdrKQGVPSCPQCR 47
RING-HC_RAD18 cd16529
RING finger, HC subclass, found in postreplication repair protein RAD18 and similar proteins; ...
728-775 5.79e-04

RING finger, HC subclass, found in postreplication repair protein RAD18 and similar proteins; RAD18, also known as HR18 or RING finger protein 73 (RNF73), is an E3 ubiquitin-protein ligase involved in post replication repair of UV-damaged DNA via its recruitment to stalled replication forks. It associates to the E2 ubiquitin conjugating enzyme UBE2B to form the UBE2B-RAD18 ubiquitin ligase complex involved in mono-ubiquitination of DNA-associated PCNA on K164. It also interacts with another E2 ubiquitin conjugating enzyme RAD6 to form a complex that monoubiquitinates proliferating cell nuclear antigen at stalled replication forks in DNA translesion synthesis. Moreover, Rad18 is a key factor in double-strand break DNA damage response (DDR) pathways via its association with K63-linked polyubiquitylated chromatin proteins. It can function as a mediator for DNA damage response signals to activate the G2/M checkpoint in order to maintain genome integrity and cell survival after ionizing radiation (IR) exposure. RAD18 contains a C3HC4-type RING-HC finger, a ubiquitin-binding zinc finger domain (UBZ), a SAP (SAF-A/B, Acinus and PIAS) domain, and a RAD6-binding domain (R6BD).


Pssm-ID: 438192 [Multi-domain]  Cd Length: 54  Bit Score: 38.44  E-value: 5.79e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 124430766 728 LEQSFMCVCCQELV-YQPVTTECFHNVCKDCLQR--SFKAQvfsCPACRHD 775
Cdd:cd16529    1 LDDLLRCPICFEYFnTAMMITQCSHNYCSLCIRRflSYKTQ---CPTCRAA 48
Ubl_NEDD8 cd01806
ubiquitin-like (Ubl) domain found in neural precursor cell expressed developmentally ...
3-63 5.91e-04

ubiquitin-like (Ubl) domain found in neural precursor cell expressed developmentally down-regulated protein 8 (NEDD8) and similar proteins; NEDD8, also termed Neddylin, or RELATED TO UBIQUITIN (RUB/Rub1p) in plant and yeast, is a ubiquitin-like protein that conjugates to nuclear proteins in a manner analogous to ubiquitination and sentrinization. It modifies a family of molecular scaffold proteins called cullins that are responsible for assembling the ROC1/Rbx1 RING-based E3 ubiquitin ligases, of which several play a direct role in tumorigenesis. NEDD8 deamidation and its inhibition of Cullin-RING ubiquitin ligases (CRLs) activity are responsible for Cycle-inhibiting factor (Cif)/Cif homolog in Burkholderia pseudomallei (CHBP)-induced cytopathic effect. NEDD8 contains a single conserved ubiquitin-like (Ubl) domain with a beta-grasp Ubl fold, a common structure involved in protein-protein interactions. Polyubiquitination, signals for a diverse set of cellular events via different isopeptide linkages formed between the C terminus of one ubiquitin (Ub) and the epsilon-amine of K6, K11, K27, K29, K33, K48, or K63 of a second Ub. Ubl NEDD8, contains many of the same lysines (K6, K11, K27, K33, K48) as Ub, where K27 has an role (other than conjugation) in the mechanism of protein neddylation.


Pssm-ID: 340504  Cd Length: 74  Bit Score: 38.91  E-value: 5.91e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 124430766   3 IQVRTIDGsqtRTIE-DVSRKATIEELRERVWALFDVRPECQRLFYRGKQLENGYTLFDYDV 63
Cdd:cd01806    1 IKVKTLTG---KEIEiDIEPTDKVERIKERVEEKEGIPPQQQRLIFSGKQMNDEKTAADYKI 59
Ubl_Rad23 cd01805
ubiquitin-like (Ubl) domain found in the Rad23 protein family; The Rad23 family includes the ...
1-73 6.35e-04

ubiquitin-like (Ubl) domain found in the Rad23 protein family; The Rad23 family includes the yeast nucleotide excision repair (NER) proteins, Rad23p (in Saccharomyces cerevisiae) and Rhp23p (in Schizosaccharomyces pombe), their mammalian orthologs HR23A and HR23B, and putative DNA repair proteins from plants. Rad23 proteins play dual roles in DNA repair as well as in proteosomal degradation. They have affinity for both the proteasome and ubiquitinylated proteins and participate in translocating polyubiquitinated proteins to the proteasome. Rad23 proteins carry an ubiquitin-like (Ubl) domain with a beta-grasp Ubl fold, and two ubiquitin-associated (UBA) domains, as well as a xeroderma pigmentosum group C (XPC) protein-binding domain. The Ubl domain is responsible for the binding to proteasome. The UBA domains are important for binding of ubiquitin (Ub) or multi-ubiquitinated substrates, which suggests Rad23 proteins might be involved in certain pathways of Ub metabolism. Both the Ubl domain and the XPC-binding domain are necessary for efficient NER function of Rad23 proteins.


Pssm-ID: 340503 [Multi-domain]  Cd Length: 72  Bit Score: 38.69  E-value: 6.35e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 124430766   1 MWIQVRTIDGsQTRTIEdVSRKATIEELRERV---WALFDvrPECQRLFYRGKQLENGYTLFDYDVGLNDIIQLLV 73
Cdd:cd01805    1 MKITFKTLQQ-QTFEIE-VEPSDTVLELKEKIeqeQGDFP--ASGQKLIYSGKVLKDDKTLSEYNIKEKDFVVVMV 72
RING-HC_TRIM3 cd16768
RING finger, HC subclass, found in tripartite motif-containing protein 3 (TRIM3); TRIM3, also ...
729-773 6.48e-04

RING finger, HC subclass, found in tripartite motif-containing protein 3 (TRIM3); TRIM3, also known as brain-expressed RING finger protein (BERP), RING finger protein 97 (RNF97), or RING finger protein 22 (RNF22), is an E3 ubiquitin-protein ligase involved in the pathogenesis of various cancers. It functions as a tumor suppressor that regulates asymmetric cell division in glioblastoma. It binds to the cdk inhibitor p21(WAF1/CIP1) and regulates its availability that promotes cyclin D1-cdk4 nuclear accumulation. Moreover, TRIM3 plays an important role in the central nervous system (CNS). It is encoded by the gene BERP (brain-expressed RING finger protein), a unique p53-regulated gene that modulates seizure susceptibility and GABAAR cell surface expression. Furthermore, TRIM3 mediates activity-dependent turnover of postsynaptic density (PSD) scaffold proteins GKAP/SAPAP1 and is a negative regulator of dendritic spine morphology. In addition, TRIM3 may be involved in vesicular trafficking via its association with the cytoskeleton-associated-recycling or transport (CART) complex that is necessary for efficient transferrin receptor recycling, but not for epidermal growth factor receptor (EGFR) degradation. It also regulates the motility of the kinesin superfamily protein KIF21B. TRIM3 belongs to the C-VII subclass of the TRIM (tripartite motif)-NHL family that is defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil domain, as well as a NHL (named after proteins NCL-1, HT2A and Lin-41 that contain repeats folded into a six-bladed beta propeller) repeat domain positioned C-terminal to the RBCC domain.


Pssm-ID: 438424 [Multi-domain]  Cd Length: 48  Bit Score: 38.06  E-value: 6.48e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 124430766 729 EQSFMCVCCQELVYQPVTTECFHNVCKDCLQRSFKAQ--VFSCPACR 773
Cdd:cd16768    2 KQFLVCSICLDRYHNPKVLPCLHTFCERCLQNYIPPQslTLSCPVCR 48
RING-HC_MuRF2 cd16760
RING finger, HC subclass, found in muscle-specific RING finger protein 2 (MuRF-2) and similar ...
729-775 6.69e-04

RING finger, HC subclass, found in muscle-specific RING finger protein 2 (MuRF-2) and similar proteins; MuRF-2, also known as tripartite motif-containing protein 55 (TRIM55) or RING finger protein 29 (RNF29), is a muscle-specific E3 ubiquitin-protein ligase in ubiquitin-mediated muscle protein turnover and is also a ligand of the transactivation domain of the serum response transcription factor (SRF). It is predominantly slow-fibre associated and highly expressed in embryonic skeletal muscle. MuRF-2 associates transiently with microtubules, myosin, and titin during sarcomere assembly. It has been implicated in microtubule, intermediate filament, and sarcomeric M-line maintenance in striated muscle development, as well as in signaling from the sarcomere to the nucleus. It plays an important role in the earliest stages of skeletal muscle differentiation and myofibrillogenesis. It is developmentally downregulated and is assembled at the M-line region of the sarcomere and with microtubules. MuRF-2 belongs to the C-II subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox2, and a coiled coil region, as well as a COS (carboxyl-terminal subgroup one signature) box, and an acidic residue-rich (AR) domain. It also harbors a MURF family-specific conserved box (MFC) between its RING-HC finger and Bbox domains.


Pssm-ID: 438417 [Multi-domain]  Cd Length: 64  Bit Score: 38.43  E-value: 6.69e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 124430766 729 EQSFMCVCCQELVYQPVTT-ECFHNVCKDCLQRSFKAQ----------------VFSCPACRHD 775
Cdd:cd16760    1 EKQLICPICLEMFTKPVVIlPCQHNLCRKCANDIFQASnpylptrggttvasggRFRCPSCRHE 64
RING-HC_RNF20 cd16814
RING finger, HC subclass, found in RING finger protein 20 (RNF20); RNF20, also known as BRE1A ...
725-779 7.08e-04

RING finger, HC subclass, found in RING finger protein 20 (RNF20); RNF20, also known as BRE1A or BRE1, is an E3 ubiquitin-protein ligase that forms a heterodimeric complex together with BRE1B, also known as RNF40, to facilitate the K120 monoubiquitination of histone H2B (H2Bub1), a DNA damage-induced histone modification that is crucial for recruitment of the chromatin remodeler SNF2h to DNA double-strand break (DSB) damage sites. It regulates the cell cycle and differentiation of neural precursor cells (NPCs), and links histone H2B ubiquitylation with inflammation and inflammation-associated cancer. Moreover, RNF20 promotes the polyubiquitination and proteasome-dependent degradation of transcription factor activator protein 2alpha (AP-2alpha), a negative regulator of adipogenesis by repressing the transcription of CCAAT/enhancer binding protein (C/EBPalpha) gene. Furthermore, RNF20 functions as an additional chromatin regulator that is necessary for mixed-lineage leukemia (MLL)-fusion-mediated leukemogenesis. It also inhibits TFIIS-facilitated transcriptional elongation to suppress pro-oncogenic gene expression. TFIIS is a factor capable of relieving stalled RNA polymerase II. RNF20 contains a C3HC4-type RING-HC finger at its C-terminus.


Pssm-ID: 438463 [Multi-domain]  Cd Length: 75  Bit Score: 38.87  E-value: 7.08e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 124430766 725 LKKLEQSFMCVCCQELVYQPVTTECFHNVCKDCLQRSFKAQVFSCPACRHDLGQN 779
Cdd:cd16814   13 IKDYKARLTCPCCNMRKKDAVLTKCFHVFCFECVKTRYDTRQRKCPKCNAAFGAN 67
COG5222 COG5222
Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only];
703-803 7.12e-04

Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only];


Pssm-ID: 227547 [Multi-domain]  Cd Length: 427  Bit Score: 42.81  E-value: 7.12e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124430766 703 EDCQNQKLWDEVLASLVEGPNFLKKLEQ---SFMCVCCQELVYQPVTTE-CFHNVCKDCLQRSFKAQVFSCPACrhdlgq 778
Cdd:COG5222  243 PDVQSWEKYQQRTKAVAEIPDQVYKMQPpniSLKCPLCHCLLRNPMKTPcCGHTFCDECIGTALLDSDFKCPNC------ 316
                         90       100
                 ....*....|....*....|....*
gi 124430766 779 nyvmvlnETLQTLLDLFFPGYSKGR 803
Cdd:COG5222  317 -------SRKDVLLDGLTPDIDKKL 334
RING-HC_SpRad8-like cd16572
RING finger, HC subclass, found in Schizosaccharomyces pombe DNA repair protein Rad8 (SpRad8) ...
735-773 7.22e-04

RING finger, HC subclass, found in Schizosaccharomyces pombe DNA repair protein Rad8 (SpRad8) and similar proteins; SpRad8 is a conserved protein homologous to Saccharomyces cerevisiae DNA repair protein Rad5 and human helicase-like transcription factor (HLTF) that is required for error-free postreplication repair by contributing to polyubiquitylation of PCNA. SpRad8 contains a C3HC4-type RING-HC finger responsible for the E3 ubiquitin ligase activity, a SNF2-family helicase domain including an ATP binding site, and a family-specific HIRAN domain (HIP116, Rad5p N-terminal domain) that contributes to nuclear localization.


Pssm-ID: 438234 [Multi-domain]  Cd Length: 61  Bit Score: 38.26  E-value: 7.22e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 124430766 735 VCCQELVYQPVTTECFHNVCKDCL------QRSfKAQVFSCPACR 773
Cdd:cd16572    9 ICAEEPISELALTRCWHSACKDCLldhiefQKS-KNEVPLCPTCR 52
zf-RING_5 pfam14634
zinc-RING finger domain;
735-774 7.86e-04

zinc-RING finger domain;


Pssm-ID: 434085 [Multi-domain]  Cd Length: 43  Bit Score: 37.79  E-value: 7.86e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 124430766  735 VCCQELVY--QPVTTECFHNVCKDCLQRSFKAQVfsCPACRH 774
Cdd:pfam14634   4 KCFKELSKtrPFYLTSCGHIFCEECLTRLLQERQ--CPICKK 43
PHD1_KMT2C_like cd15509
PHD finger 1 found in Histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); KMT2C, ...
348-393 8.71e-04

PHD finger 1 found in Histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3) or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named MLL4, a fourth human homolog of Drosophila trithorax, located on chromosome 12. It enzymatically generates trimethylated histone H3 Lysine 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. KMT2D is also a part of ASCOM. Both KMT2C and KMT2D contain the catalytic domain SET, several plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions. This model corresponds to the first PHD finger.


Pssm-ID: 276984  Cd Length: 48  Bit Score: 37.67  E-value: 8.71e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 124430766 348 CHKCGEKRDPNMQLLCDECNMAYHIYCLSPPLDKVPEEEY-WYCPSC 393
Cdd:cd15509    2 CAVCDSPGDLSDLLFCTSCGQHYHGSCLDPAVRPTPLVRAgWQCPEC 48
RING-HC_TRIM26_C-IV cd16598
RING finger, HC subclass, found in tripartite motif-containing protein 26 (TRIM26) and similar ...
728-773 9.44e-04

RING finger, HC subclass, found in tripartite motif-containing protein 26 (TRIM26) and similar proteins; TRIM26, also known as acid finger protein (AFP), RING finger protein 95 (RNF95), or zinc finger protein 173 (ZNF173), is an E3 ubiquitin-protein ligase that negatively regulates interferon-beta production and antiviral response through polyubiquitination and degradation of nuclear transcription factor IRF3. It functions as an important regulator for RNA virus-triggered innate immune response by bridging TBK1 to NEMO (NF-kappaB essential modulator, also known as IKKgamma) and mediating TBK1 activation. It also acts as a novel tumor suppressor of hepatocellular carcinoma by regulating cancer cell proliferation, colony forming ability, migration, and invasion. TRIM26 belongs the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, a B-box, and two coiled coil domains, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain.


Pssm-ID: 438260 [Multi-domain]  Cd Length: 64  Bit Score: 38.22  E-value: 9.44e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 124430766 728 LEQSFMCVCCQELVYQPVTTECFHNVCKDCL----QRSFKAQVFSCPACR 773
Cdd:cd16598    1 LEEEVTCSICLDYLRDPVTIDCGHNFCRSCItdycPISGGHERPVCPLCR 50
COG3440 COG3440
Predicted restriction endonuclease [Defense mechanisms];
447-619 9.86e-04

Predicted restriction endonuclease [Defense mechanisms];


Pssm-ID: 225973 [Multi-domain]  Cd Length: 301  Bit Score: 42.11  E-value: 9.86e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124430766 447 HYGPIPGIPVGSTWRFRVQVSEAGVHRPHVGGIHGRSNDGAYSLVLAGGFEDEVDRGDEFTYTGSGGKNLAGnkRIGAPs 526
Cdd:COG3440    5 NYYAKSFSQRNASLKIFGGNREAAPHKPILLLDVGRKISTFFITENQGIYETELIEPFIQLWSFFGPKLQKY--GVDAP- 81
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124430766 527 adQTLTNMNRALALNCDAPLDDkigaesrnwragkpvRVIRSFkgRKISKYAPEEGNRYDGIYKVVKYWPEISSSHgFLV 606
Cdd:COG3440   82 --FELLQGDGKWHLDIKEGFDG---------------LSIRTL--PTEKEFVEYHYIDDELEQSLQYHQGEKRLID-DLI 141
                        170
                 ....*....|....*
gi 124430766 607 WRYLLRR--DDVEPA 619
Cdd:COG3440  142 SIWRKEVlqEDIEEL 156
RING-HC_TRIM41-like_C-IV cd16602
RING finger, HC subclass, found in tripartite motif-containing proteins TRIM41, TRIM52 and ...
729-778 1.03e-03

RING finger, HC subclass, found in tripartite motif-containing proteins TRIM41, TRIM52 and similar proteins; TRIM41 and TRIM52, two closely related tripartite motif-containing proteins, have dramatically expanded RING domains compared with the rest of the TRIM family proteins. TRIM41 belongs to the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain. In contrast, TRIM52 lacks the putative viral recognition SPRY/B30.2 domain, and thus has been classified to the C-V subclass of the TRIM family that contains only RBCC domains. TRIM41, also known as RING finger-interacting protein with C kinase (RINCK), is an E3 ubiquitin-protein ligase that promotes the ubiquitination of protein kinase C (PKC) isozymes in cells. It specifically recognizes the C1 domain of PKC isozymes. It controls the amplitude of PKC signaling by controlling the amount of PKC in the cell. TRIM52, also known as RING finger protein 102 (RNF102), is encoded by a novel, noncanonical antiviral TRIM52 gene in primate genomes with unique specificity determined by the rapidly evolving RING domain.


Pssm-ID: 438264 [Multi-domain]  Cd Length: 53  Bit Score: 37.60  E-value: 1.03e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 124430766 729 EQSFMCVCCQELVYQPVTTECFHNVCKDCLQRSFKaqvFSCPACRHDLGQ 778
Cdd:cd16602    1 QEEAVCAICLDYFKDPVSIGCGHNFCRVCVTQLWG---FTCPQCRKSFPR 47
PHD_BRPF_JADE_like cd15492
PHD finger found in BRPF proteins, Jade proteins, protein AF-10, AF-17, and similar proteins; ...
348-393 1.06e-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: 37.60  E-value: 1.06e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 124430766 348 CHKC--GEKRDPNMQLLCDECNMAYHIYCLSppLDKVPEEEyWYCPSC 393
Cdd:cd15492    2 CDVCldGESEDDNEIVFCDGCNVAVHQSCYG--IPLIPEGD-WFCRKC 46
RING-HC_PCGF5 cd16737
RING finger found in polycomb group RING finger protein 5 (PCGF5) and similar proteins; PCGF5, ...
734-798 1.07e-03

RING finger found in polycomb group RING finger protein 5 (PCGF5) and similar proteins; PCGF5, also known as RING finger protein 159 (RNF159), is one of six PcG RING finger (PCGF) homologs (PCGF1/NSPc1, PCGF2/Mel-18, PCGF3, PCGF4/BMI1, PCGF5, and PCGF6/MBLR) and serves as the core component of a Polycomb repressive complex 1 (PRC1). Like other PCGF homologs, PCGF5 associates with ring finger protein 2 (RNF2) to form a RNF2-PCGF heterodimer, which is catalytically competent as an E3 ubiquitin transferase and is the scaffold for the assembly of additional components. PCGF5 contains a C3HC4-type RING-HC finger.


Pssm-ID: 438395 [Multi-domain]  Cd Length: 95  Bit Score: 38.97  E-value: 1.07e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 124430766 734 CVCCQELVYQPVT-TECFHNVCKDCLQRSFKAQVFsCPACRHDLG--QNYVMV-LNETLQTLLDLFFPG 798
Cdd:cd16737   13 CRICKGYLIKPTTvTECLHTFCKSCIVQHFEDSND-CPECGIQVHetNPLEMLrLDNTLEEIIFKLVPG 80
zf-RING_2 pfam13639
Ring finger domain;
732-773 1.09e-03

Ring finger domain;


Pssm-ID: 433370 [Multi-domain]  Cd Length: 44  Bit Score: 37.39  E-value: 1.09e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 124430766  732 FMCVCCQELV---YQPVTTECFHNVCKDCLQRSFKAQvFSCPACR 773
Cdd:pfam13639   1 DECPICLEEFeegDKVVVLPCGHHFHRECLDKWLRSS-NTCPLCR 44
RING-HC_ScRAD18-like cd23148
RING finger, HC subclass, found in Saccharomyces cerevisiae radiation sensitivity protein 18 ...
729-776 1.11e-03

RING finger, HC subclass, found in Saccharomyces cerevisiae radiation sensitivity protein 18 (RAD18) and similar proteins; RAD18, also called RING-type E3 ubiquitin transferase RAD18, acts as a postreplication repair E3 ubiquitin-protein ligase that associates with the E2 ubiquitin conjugating enzyme UBC2/RAD6 to form the UBC2-RAD18 ubiquitin ligase complex involved in postreplicative repair (PRR) of damaged DNA. The UBC2-RAD18 complex cooperates with RAD5 and the UBC13-MMS2 dimer to attach mono-ubiquitin chains on 'Lys-164' of POL30, which is necessary for PRR. The UBC2-RAD18 complex is also involved in prevention of spontaneous mutations caused by 7,8-dihydro-8-oxoguanine. RAD18 is an E3 RING-finger protein belonging to the UBC2/RAD6 epistasis group. It contains a typical C3HC4-type RING-HC finger.


Pssm-ID: 438510 [Multi-domain]  Cd Length: 52  Bit Score: 37.51  E-value: 1.11e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 124430766 729 EQSFMCVCCQELVYQPVTTECFHNVCKDCLQRSFKAQVfSCPACRHDL 776
Cdd:cd23148    1 DHALRCHICKDLLKAPMRTPCNHTFCSFCIRTHLNNDA-RCPLCKAEV 47
PHD3_KDM5A_like cd15610
PHD finger 3 found in Lysine-specific demethylase 5A (KDM5A), 5B (KDM5B), and similar proteins; ...
345-393 1.17e-03

PHD finger 3 found in Lysine-specific demethylase 5A (KDM5A), 5B (KDM5B), and similar proteins; The family includes KDM5A and KDM5B, both of which belong to the JARID subfamily within the JmjC proteins. KDM5A, also termed Histone demethylase JARID1A, or 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 the trimethylated histone H3 lysine 4 (H3K4me3) demethylase. It also displays DNA-binding activities that can recognize the specific DNA sequence CCGCCC. KDM5B, also termed Cancer/testis antigen 31 (CT31), or Histone demethylase JARID1B, or Jumonji/ARID domain-containing protein 1B (JARID1B), or PLU-1, or retinoblastoma-binding protein 2 homolog 1 (RBP2-H1 or RBBP2H1A), 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 asTIEG1/KLF10 (transforming growth factor-beta inducible early gene-1/Kruppel-like transcription factor 10), and possibly function as a transcriptional corepressor. The family also includes the 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 three plant homeodomain (PHD) fingers. This model corresponds to the third PHD finger.


Pssm-ID: 277083 [Multi-domain]  Cd Length: 50  Bit Score: 37.31  E-value: 1.17e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 124430766 345 MCS---CHK-CGEKRDpnmQLLCDECNMAYHIYCLSPPLDKVPEEEYWYCPSC 393
Cdd:cd15610    1 SCSakqCLKpTGDEVN---WVQCDGCEEWFHLLCVGLSPEEVAEDEDYICPSC 50
RING-HC_MuRF1 cd16759
RING finger, HC subclass, found in muscle-specific RING finger protein 1 (MuRF-1) and similar ...
729-774 1.37e-03

RING finger, HC subclass, found in muscle-specific RING finger protein 1 (MuRF-1) and similar proteins; MuRF-1, also known as tripartite motif-containing protein 63 (TRIM63), RING finger protein 28 (RNF28), iris RING finger protein, or striated muscle RING zinc finger, is an E3 ubiquitin-protein ligase in ubiquitin-mediated muscle protein turnover. It is predominantly fast (type II) fibre-associated in skeletal muscle and can bind to many myofibrillar proteins, including titin, nebulin, the nebulin-related protein NRAP, troponin-I (TnI), troponin-T (TnT), myosin light chain 2 (MLC-2), myotilin, and T-cap. The early and robust upregulation of MuRF-1 is triggered by disuse, denervation, starvation, sepsis, or steroid administration resulting in skeletal muscle atrophy. It also plays a role in maintaining titin M-line integrity. It associates with the periphery of the M-line lattice and may be involved in the regulation of the titin kinase domain. It also participates in muscle stress response pathways and gene expression. MuRF-1 belongs to the C-II subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox2, and a coiled coil region, as well as a COS (carboxyl-terminal subgroup one signature) box, and an acidic residue-rich (AR) domain. It also harbors a MURF family-specific conserved box (MFC) between its RING-HC finger and Bbox domains.


Pssm-ID: 319673 [Multi-domain]  Cd Length: 63  Bit Score: 37.70  E-value: 1.37e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 124430766 729 EQSFMCVCCQELVYQPVTT-ECFHNVCKDCLQRSFKAQ----------------VFSCPACRH 774
Cdd:cd16759    1 EKQLICPICLEMFTKPVVIlPCQHNLCRKCANDIFQAAnpywqsrgtsmlgsggRFRCPSCRH 63
PHD1_MTF2 cd15578
PHD finger 1 found in metal-response element-binding transcription factor 2 (MTF2); MTF2, also ...
342-393 1.41e-03

PHD finger 1 found in metal-response element-binding transcription factor 2 (MTF2); MTF2, also termed metal regulatory transcription factor 2, or metal-response element DNA-binding protein M96, or polycomb-like protein 2 (PCL2), complexes with the polycomb repressive complex-2 (PRC2) in embryonic stem cells and regulates the transcriptional networks during embryonic stem cell self-renewal and differentiation. It recruits the PRC2 complex to the inactive X chromosome and target loci in embryonic stem cells. Moreover, MTF2 is required for PRC2-mediated Hox cluster repression. It activates the Cdkn2a gene and promotes cellular senescence, thus suppressing the catalytic activity of PRC2 locally. MTF2 consists of an N-terminal Tudor domain followed by two PHD fingers, and a C-terminal MTF2 domain. This model corresponds to the first PHD finger.


Pssm-ID: 277053  Cd Length: 53  Bit Score: 37.37  E-value: 1.41e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 124430766 342 TCHMCschKCGEKRDPNMQLLCDECNMAYHIYCLSPPLDKV--PEEEYWYCPSC 393
Cdd:cd15578    1 VCTVC---QDGSSESPNEIVLCDKCGQGYHQLCHNPKIDSSvlDPDVPWLCRQC 51
RING-HC_TRIM58_C-IV cd16606
RING finger, HC subclass, found in tripartite motif-containing protein TRIM58 and similar ...
734-773 1.49e-03

RING finger, HC subclass, found in tripartite motif-containing protein TRIM58 and similar proteins; TRIM58, also known as protein BIA2, is an erythroid E3 ubiquitin-protein ligase induced during late erythropoiesis. It binds and ubiquitinates the intermediate chain of the microtubule motor dynein (DYNC1LI1/DYNC1LI2), stimulating the degradation of the dynein holoprotein complex. It may participate in the erythroblast enucleation process through regulation of nuclear polarization. TRIM58 belongs to the C-IV subclass of TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain.


Pssm-ID: 438268 [Multi-domain]  Cd Length: 53  Bit Score: 37.15  E-value: 1.49e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 124430766 734 CVCCQELVYQPVTTECFHNVCKDCL----QRSFKAQ--VFSCPACR 773
Cdd:cd16606    5 CPVCLDFLQEPVSVDCGHSFCLRCIsefcEKSDSAQggVYACPQCR 50
Ubl_UBTD cd01794
ubiquitin-like (Ubl) domain found in ubiquitin domain-containing proteins UBTD1, UBTD2, and ...
19-73 1.89e-03

ubiquitin-like (Ubl) domain found in ubiquitin domain-containing proteins UBTD1, UBTD2, and similar proteins; This family represents a group of ubiquitin-like (Ubl) domain-containing proteins evolutionarily conserved and found in metazoa, fungi, and plants. They may regulate the activity and/or specificity of E2 ubiquitin conjugating enzymes belonging to the UBE2D family. Members in this family contain an N-terminal ubiquitin binding domain (UBD) and a C-terminal Ubl domain with a beta-grasp Ubl fold, a common structure involved in protein-protein interactions.


Pssm-ID: 340492  Cd Length: 69  Bit Score: 37.27  E-value: 1.89e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 124430766  19 VSRKATIEELRERVWALFDVRPECQRLFYRGKQLENGYTLFDYDVGLNDIIQLLV 73
Cdd:cd01794   15 VRSTDTVLQAKRRLQALEGIEPSRQRWFFSGKLLTDKTRIEDAKIPKGFVVQVIV 69
Ubl_Dsk2p_like cd16106
ubiquitin-like (Ubl) domain found in Saccharomyces cerevisiae proteasome interacting protein ...
18-63 1.98e-03

ubiquitin-like (Ubl) domain found in Saccharomyces cerevisiae proteasome interacting protein Dsk2p and similar proteins; The family contains several fungal multiubiquitin receptors, including Saccharomyces cerevisiae Dsk2p and Schizosaccharomyces pombe Dph1p, both of which have been characterized as shuttle proteins transporting ubiquitinated substrates destined for degradation from the E3 ligase to the 26S proteasome. They interact with the proteasome through their N-terminal ubiquitin-like domain (Ubl) and with ubiquitin (Ub) through their C-terminal Ub-associated domain (UBA). S. cerevisiae Dsk2p is a nuclear-enriched protein that may involve in the ubiquitin-proteasome proteolytic pathway through interacting with K48-linked polyubiquitin and the proteasome. Moreover, it has been implicated in spindle pole duplication through assisting in Cdc31 assembly into the new spindle pole body (SPB). S. pombe Dph1p is an ubiquitin (Ub0 receptor working in concert with the class V myosin, Myo52, to target the degradation of the S. pombe CLIP-170 homolog, Tip1. It also can protect Ub chains against disassembly by deubiquitinating enzymes.


Pssm-ID: 340523  Cd Length: 73  Bit Score: 37.62  E-value: 1.98e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 124430766  18 DVSRKATIEELRERVWALFDVRPECQRLFYRGKQLENGYTLFDYDV 63
Cdd:cd16106   16 EVEPDATVLELKELIAEKSDIPAEQQRLIYKGKILKDEETLSSYKI 61
zf-C3HC4_2 pfam13923
Zinc finger, C3HC4 type (RING finger);
733-772 2.01e-03

Zinc finger, C3HC4 type (RING finger);


Pssm-ID: 404756 [Multi-domain]  Cd Length: 40  Bit Score: 36.65  E-value: 2.01e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 124430766  733 MCVCCQELVYQP-VTTECFHNVCKDCLQRSFKAQVfSCPAC 772
Cdd:pfam13923   1 MCPICMDMLKDPsTTTPCGHVFCQDCILRALRAGN-ECPLC 40
RING-HC_TRIM2 cd16767
RING finger, HC subclass, found in tripartite motif-containing protein 2 (TRIM2); TRIM2, also ...
729-774 2.12e-03

RING finger, HC subclass, found in tripartite motif-containing protein 2 (TRIM2); TRIM2, also known as RING finger protein 86 (RNF86), is an E3 ubiquitin-protein ligase that ubiquitinates the neurofilament light chain, a component of the intermediate filament in axons. Loss of function of TRIM2 results in early-onset axonal neuropathy. TRIM2 also plays a role in mediating the p42/p44 MAPK-dependent ubiquitination of the cell death-promoting protein Bcl-2-interacting mediator of cell death (Bim) in rapid ischemic tolerance. TRIM2 belongs to the C-VII subclass of the TRIM (tripartite motif)-NHL family that is defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil domain, as well as a NHL (named after proteins NCL-1, HT2A and Lin-41 that contain repeats folded into a six-bladed beta propeller) repeat domain positioned C-terminal to the RBCC domain.


Pssm-ID: 438423 [Multi-domain]  Cd Length: 51  Bit Score: 36.92  E-value: 2.12e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 124430766 729 EQSFMCVCCQELVYQPVTTECFHNVCKDCLQRSFKAQ--VFSCPACRH 774
Cdd:cd16767    4 KQFLICSICLDRYKNPKVLPCLHTFCERCLQNYIPAHslTLSCPVCRQ 51
PHD_BRPF2 cd15677
PHD finger found in bromodomain and PHD finger-containing protein 2 (BRPF2) and similar ...
340-393 2.22e-03

PHD finger found in bromodomain and PHD finger-containing protein 2 (BRPF2) and similar proteins; BRPF2, also termed bromodomain-containing protein 1 (BRD1), or BR140-like protein, is encoded by BRL (BR140 Like gene). It is responsible for the bulk of the acetylation of H3K14 and forms a novel monocytic leukemic zinc-finger protein (MOZ)/MOZ-related factor (MORF) H3 histone acetyltransferase (HAT) complex with HBO1 and ING4. The complex is required for full transcriptional activation of the erythroid-specific regulator genes essential for terminal differentiation and survival of erythroblasts in fetal liver. BRPF2 shows widespread expression and localizes to the nucleus within spermatocytes. It contains a cysteine rich region harboring a canonical Cys4HisCys3 plant homeodomain (PHD) finger followed by a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, a bromodomain, and a proline-tryptophan-tryptophan-proline (PWWP) domain. This model corresponds to the canonical Cys4HisCys3 PHD finger.


Pssm-ID: 277147 [Multi-domain]  Cd Length: 54  Bit Score: 36.91  E-value: 2.22e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 124430766 340 DKTCHMCschKCGEKRDPNMQLLCDECNMAYHIYCLSPPldKVPEEEyWYCPSC 393
Cdd:cd15677    1 DAVCCIC---MDGECQNSNVILFCDMCNLAVHQECYGVP--YIPEGQ-WLCRHC 48
vRING-HC-C4C4_RBBP6 cd16620
Variant RING finger, HC subclass (C4C4-type), found in retinoblastoma-binding protein 6 (RBBP6) ...
732-776 2.50e-03

Variant RING finger, HC subclass (C4C4-type), found in retinoblastoma-binding protein 6 (RBBP6) and similar proteins; RBBP6, also known as proliferation potential-related protein, protein P2P-R, retinoblastoma-binding Q protein 1 (RBQ-1), or p53-associated cellular protein of testis (PACT), is a nuclear E3 ubiquitin-protein ligase involved in multiple processes, such as the control of gene expression, mitosis, cell differentiation, and cell apoptosis. It plays a role in both promoting and inhibiting apoptosis in many human cancers, including esophageal, lung, hepatocellular, and colon cancers, familial myeloproliferative neoplasms, as well as in human immunodeficiency virus-associated nephropathy (HIVAN). It functions as an Rb- and p53-binding protein that plays an important role in chaperone-mediated ubiquitination and possibly in protein quality control. It acts as a scaffold protein to promote the assembly of the p53/TP53-MDM2 complex, resulting in an increase of MDM2-mediated ubiquitination and degradation of p53/TP53, and leading to both apoptosis and cell growth. It is also a double-stranded RNA-binding protein that plays a role in mRNA processing by regulating the human polyadenylation machinery and modulating expression of mRNAs with AU-rich 3' untranslated regions (UTRs). Moreover, RBBP6 ubiquitinates and destabilizes the transcriptional repressor ZBTB38 that negatively regulates transcription and levels of the MCM10 replication factor on chromatin. Furthermore, RBBP6 is involved in tunicamycin-induced apoptosis by mediating protein kinase (PKR) activation. RBBP6 contains an N-terminal ubiquitin-like domain and a C4C4-type RING finger, whose overall folding is similar to that of the typical C3HC4-type RING-HC finger. RBBP6 interacts with chaperones Hsp70 and Hsp40 through its N-terminal ubiquitin-like domain. It promotes the ubiquitination of p53 by Hdm2 in an E4-like manner through its RING finger. It also interacts directly with the pro-proliferative transcription factor Y-box-binding protein-1 (YB-1) via its RING finger.


Pssm-ID: 438282 [Multi-domain]  Cd Length: 55  Bit Score: 36.61  E-value: 2.50e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 124430766 732 FMCVCCQELVYQPVTTECFHNV-CKDCLQRSFKAQVFSCPACRHDL 776
Cdd:cd16620    4 LKCPICKDLMKDAVLTPCCGNSfCDECIRTALLEEDFTCPTCKEPD 49
RING-HC_MSL2 cd16522
RING finger found in Drosophila melanogaster male-specific lethal-2 (MSL2) and similar ...
728-758 2.55e-03

RING finger found in Drosophila melanogaster male-specific lethal-2 (MSL2) and similar proteins; MSL2, also known as RING finger protein 184 (RNF184), is a putative DNA-binding protein required for X chromosome dosage compensation in Drosophila males. Its expression is sex specifically regulated by Sex-lethal. Drosophila dosage compensation proteins MOF, MSL1, MSL2, and MSL3 are essential for elevating transcription of the single X chromosome in the male (X chromosome dosage compensation). MSL2 plays a critical role in translation and/or stability of MSL1 in males. In complex with MSL1, it acts as an E3 ubiquitin ligase that promotes ubiquitination of histone H2B. MSL2 contains a C3HC4-type RING-HC finger and a metallothionein-like domain with eight conserved and two non-conserved cysteines, as well as a positively and a negatively charged amino acid residue cluster and a coiled coil domain that may be involved in protein-protein interactions. This subfamily also includes many male-specific lethal-2 homologs from bilaterians.


Pssm-ID: 438185  Cd Length: 60  Bit Score: 36.65  E-value: 2.55e-03
                         10        20        30
                 ....*....|....*....|....*....|....
gi 124430766 728 LEQSFMC-VCCQELV--YQPVTTECFHNVCKDCL 758
Cdd:cd16522    2 LRQALSCcVCGQLLVdpIGPTNSTCQHNVCKGCK 35
PHD_BRPF1 cd15676
PHD finger found in bromodomain and PHD finger-containing protein 1 (BRPF1) and similar ...
338-401 2.59e-03

PHD finger found in bromodomain and PHD finger-containing protein 1 (BRPF1) and similar proteins; BRPF1, also termed peregrin or protein Br140, is a multi-domain protein that binds histones, mediates monocytic leukemic zinc-finger protein (MOZ)-dependent histone acetylation, and is required for Hox gene expression and segmental identity. It is a close partner of the MOZ histone acetyltransferase (HAT) complex and a novel Trithorax group (TrxG) member with a central role during development. BRPF1 is primarily a nuclear protein that has a broad tissue distribution and is abundant in testes and spermatogonia. It contains 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. BRPF1 may be involved in chromatin remodeling. This model corresponds to the canonical Cys4HisCys3 PHD finger.


Pssm-ID: 277146 [Multi-domain]  Cd Length: 62  Bit Score: 36.96  E-value: 2.59e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 124430766 338 DPDKTCHMCSChkcGEKRDPNMQLLCDECNMAYHIYCLSPPLdkVPEEEyWYCPSCKTDSSEVV 401
Cdd:cd15676    5 DEDAVCCICND---GECQNSNVILFCDMCNLAVHQECYGVPY--IPEGQ-WLCRRCLQSPSRAV 62
RING-HC_SH3RF2 cd16749
RING finger, HC subclass, found in SH3 domain-containing RING finger protein 2 (SH3RF2) and ...
735-773 2.95e-03

RING finger, HC subclass, found in SH3 domain-containing RING finger protein 2 (SH3RF2) and similar proteins; SH3RF2, also known as heart protein phosphatase 1-binding protein (HEPP1), plenty of SH3s (POSH)-eliminating RING protein (POSHER), protein phosphatase 1 regulatory subunit 39, or RING finger protein 158 (RNF158), is a putative E3 ubiquitin-protein ligase that acts as an anti-apoptotic regulator for the c-Jun N-terminal kinase (JNK) pathway by binding to and promoting the proteasomal degradation of SH3RF1 (or POSH), a scaffold protein that is required for pro-apoptotic JNK activation. It may also play a role in cardiac functions together with protein phosphatase 1. SH3RF2 contains an N-terminal C3HC4-type RING-HC finger responsible for the E3 ligase activity and four Src Homology 3 (SH3) domains, which are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs.


Pssm-ID: 438407 [Multi-domain]  Cd Length: 46  Bit Score: 36.07  E-value: 2.95e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 124430766 735 VCCQELVYQPVTTECFHNVCKDCLQRSFKAQV-FSCPACR 773
Cdd:cd16749    5 VCFEKLDVTAKVLPCQHTFCKPCLQRIFKARKeLRCPECR 44
RING-HC_TRIM13_C-V cd16762
RING finger, HC subclass, found in tripartite motif-containing protein 13 (TRIM13) and similar ...
729-775 3.05e-03

RING finger, HC subclass, found in tripartite motif-containing protein 13 (TRIM13) and similar proteins; TRIM13, also known as B-cell chronic lymphocytic leukemia tumor suppressor Leu5, leukemia-associated protein 5, putative tumor suppressor RFP2, RING finger protein 77 (RNF77), or Ret finger protein 2, is an endoplasmic reticulum (ER) membrane anchored E3 ubiquitin-protein ligase that interacts with proteins localized to the ER, including valosin-containing protein (VCP), a protein indispensable for ER-associated degradation (ERAD). It also targets the known ER proteolytic substrate CD3-delta, but not the N-end rule substrate Ub-R-YFP (yellow fluorescent protein) for degradation. Moreover, TRIM13 regulates ubiquitination and degradation of NEMO to suppress tumor necrosis factor (TNF) induced nuclear factor-kappaB (NF- kappa B) activation. It is also involved in NF-kappaB p65 activation and nuclear factor of activated T-cells (NFAT)-dependent activation of c-Rel upon T-cell receptor engagement. Furthermore, TRIM13 negatively regulates melanoma differentiation-associated gene 5 (MDA5)-mediated type I interferon production. It also regulates caspase-8 ubiquitination, translocation to autophagosomes, and activation during ER stress induced cell death. Meanwhile, TRIM13 enhances ionizing radiation-induced apoptosis by increasing p53 stability and decreasing AKT kinase activity through MDM2 and AKT degradation. TRIM13 belongs to the C-V subclass of the TRIM (tripartite motif) family of proteins that are defined by an N-terminal RBCC (RING, Bbox, and coiled coil) domain, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region. In addition, TRIM13 contains a C-terminal transmembrane domain.


Pssm-ID: 438418 [Multi-domain]  Cd Length: 56  Bit Score: 36.43  E-value: 3.05e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 124430766 729 EQSFMCVCCQELVYQPVTTECFHNVCKDCLQRSFKAQV--------FSCPACRHD 775
Cdd:cd16762    1 EEDLTCPICCCLFDDPRVLPCSHNFCKKCLEGILEGNVrtmlwrppFKCPTCRKE 55
RING-HC_RNF20-like cd16704
RING finger, HC subclass, found in RING finger protein RNF20, RNF40, and similar proteins; ...
734-779 3.08e-03

RING finger, HC subclass, found in RING finger protein RNF20, RNF40, and similar proteins; RNF20, also known as BRE1A, and RNF40, also known as BRE1B, are E3 ubiquitin-protein ligases that work together to form a heterodimeric complex that facilitate the K120 monoubiquitination of histone H2B (H2Bub1), a DNA damage-induced histone modification that is crucial for recruitment of the chromatin remodeler SNF2h to DNA double-strand break (DSB) damage sites. RNF20 regulates the cell cycle and differentiation of neural precursor cells (NPCs) and links histone H2B ubiquitylation with inflammation and inflammation-associated cancer. RNF40, also known as 95 kDa retinoblastoma-associated protein (RBP95), was identified as a novel leucine zipper retinoblastoma protein (pRb)-associated protein that may function as a regulation factor in RNA polymerase II-mediated transcription and/or transcriptional processing. All subfamily members contain a C3HC4-type RING-HC finger at its C-terminus.


Pssm-ID: 438364 [Multi-domain]  Cd Length: 65  Bit Score: 36.66  E-value: 3.08e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 124430766 734 CVCCQELVYQPVTTECFHNVCKDCLQRSFKAQVFSCPACRHDLGQN 779
Cdd:cd16704   13 CPCCNTRKKDAVLTKCFHVFCFECLKTRYETRQRKCPKCNAAFGAN 58
RING-HC_TRIM10_C-IV cd16593
RING finger, HC subclass, found in tripartite motif-containing protein 10 (TRIM10) and similar ...
728-773 3.08e-03

RING finger, HC subclass, found in tripartite motif-containing protein 10 (TRIM10) and similar proteins; TRIM10, also known as B30-RING finger protein (RFB30), RING finger protein 9 (RNF9), or hematopoietic RING finger 1 (HERF1), is a novel hematopoiesis-specific RING finger protein required for terminal differentiation of erythroid cells. TRIM10 belongs to the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain.


Pssm-ID: 438255 [Multi-domain]  Cd Length: 61  Bit Score: 36.81  E-value: 3.08e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 124430766 728 LEQSFMCVCCQELVYQPVTTECFHNVCKDCLQRSFK------AQVFSCPACR 773
Cdd:cd16593    2 LADEVNCPICQGTLREPVTIDCGHNFCRACLTRYCEipgpdlEEPPTCPLCK 53
RING-HC_RFPL4B cd16623
RING finger, HC subclass, found in Ret finger protein-like 4B (RFPL4B) and similar proteins; ...
726-773 3.43e-03

RING finger, HC subclass, found in Ret finger protein-like 4B (RFPL4B) and similar proteins; RFPL4B, also called RING finger protein 211 (RNF211), is an uncharacterized RING finger protein containing a typical C3HC4-type RING-HC finger.


Pssm-ID: 438285 [Multi-domain]  Cd Length: 63  Bit Score: 36.72  E-value: 3.43e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 124430766 726 KKLEQSFMCVCCQELVYQPVTTECFHNVCKDCLQRSFKAQ---VFSCPACR 773
Cdd:cd16623    3 NRLEMEATCPICLDFFSHPISLSCAHIFCFDCIQKWMTKRedsILTCPLCR 53
RING-HC_TRIM8_C-V cd16580
RING finger, HC subclass, found in tripartite motif-containing protein 8 (TRIM8) and similar ...
728-778 3.45e-03

RING finger, HC subclass, found in tripartite motif-containing protein 8 (TRIM8) and similar proteins; TRIM8, also known as glioblastoma-expressed RING finger protein (GERP) or RING finger protein 27 (RNF27), is a probable E3 ubiquitin-protein ligase that may promote proteasomal degradation of suppressor of cytokine signaling 1 (SOCS1) and further regulate interferon-gamma signaling. It functions as a new p53 modulator that stabilizes p53 impairing its association with MDM2 and inducing the reduction of cell proliferation. TRIM8 deficit dramatically impairs p53 stabilization and activation in response to chemotherapeutic drugs. TRIM8 also modulates tumor necrosis factor-alpha (TNFalpha) and interleukin-1beta (IL-1beta)-triggered nuclear factor-kappaB (NF- kappa B) activation by targeting transforming growth factor beta (TGFbeta) activated kinase 1 (TAK1) for K63-linked polyubiquitination. Moreover, TRIM8 modulates translocation of phosphorylated STAT3 into the nucleus through interaction with Hsp90beta and consequently regulates transcription of Nanog in embryonic stem cells. It also interacts with protein inhibitor of activated STAT3 (PIAS3), which inhibits IL-6-dependent activation of STAT3. TRIM8 belongs to the C-V subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil domain, as well as an uncharacterized region positioned C-terminal to the RBCC domain. The coiled coil domain is required for homodimerization and the region immediately C-terminal to the RING motif is sufficient to mediate the interaction with SOCS1.


Pssm-ID: 438242 [Multi-domain]  Cd Length: 67  Bit Score: 36.79  E-value: 3.45e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 124430766 728 LEQSFMCVCCQELVYQPVTTECFHNVCKDCLQRSF--KAQVFSCPACRHDLGQ 778
Cdd:cd16580    8 FEEELICPICLHVFVEPVQLPCKHNFCRGCIGEAWakDAGLVRCPECNQAYNQ 60
RING-HC_TRIM13_like_C-V cd16581
RING finger, HC subclass, found in tripartite motif-containing proteins TRIM13, TRIM59 and ...
734-773 3.45e-03

RING finger, HC subclass, found in tripartite motif-containing proteins TRIM13, TRIM59 and similar proteins; TRIM13 and TRIM59, two closely related tripartite motif-containing proteins, belong to the C-V subclass of the TRIM (tripartite motif) family of proteins that are defined by an N-terminal RBCC (RING, Bbox, and coiled coil) domain, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, followed by a C-terminal transmembrane domain. TRIM13, also known as B-cell chronic lymphocytic leukemia tumor suppressor Leu5, leukemia-associated protein 5, putative tumor suppressor RFP2, RING finger protein 77 (RNF77), or Ret finger protein 2, is an endoplasmic reticulum (ER) membrane anchored E3 ubiquitin-protein ligase that interacts with proteins localized to the ER, including valosin-containing protein (VCP), a protein indispensable for ER-associated degradation (ERAD). TRIM59, also known as RING finger protein 104 (RNF104) or tumor suppressor TSBF-1, is a putative E3 ubiquitin-protein ligase that functions as a novel multiple cancer biomarker for immunohistochemical detection of early tumorigenesis.


Pssm-ID: 438243 [Multi-domain]  Cd Length: 50  Bit Score: 36.33  E-value: 3.45e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 124430766 734 CVCCQELVYQPVTTECFHNVCKDCLQRSFKAQV------FSCPACR 773
Cdd:cd16581    5 CSICYNIFDDPKILPCSHTFCKNCLEKLLAASGyyllasLKCPTCR 50
RING-HC_RNF222 cd16564
RING finger, HC subclass, found in RING finger protein 222 (RNF222) and similar proteins; ...
735-774 3.51e-03

RING finger, HC subclass, found in RING finger protein 222 (RNF222) and similar proteins; RNF222 is an uncharacterized C3HC4-type RING-HC finger-containing protein. It may function as an E3 ubiquitin-protein ligase.


Pssm-ID: 438226 [Multi-domain]  Cd Length: 50  Bit Score: 36.23  E-value: 3.51e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 124430766 735 VCCQELVYQPVTTECFHNVCKDCLQRSFKAQVFSCPACRH 774
Cdd:cd16564    5 VCYEDFDDAPRILSCGHSFCEDCLVKQLVSMTISCPICRR 44
Ubl_parkin cd01798
ubiquitin-like (Ubl) domain found in parkin and similar proteins; Parkin, also termed ...
3-75 3.58e-03

ubiquitin-like (Ubl) domain found in parkin and similar proteins; Parkin, also termed Parkinson juvenile disease protein 2, is a RBR-type E3 ubiquitin-protein ligase that is associated with recessive early onset Parkinson's disease (PD), and exerts a protective effect against dopamine-induced alpha-synuclein-dependent cell toxicity. Mutations in the parkin gene cause autosomal recessive juvenile parkinsonism. Parkin functions within a multiprotein E3 ubiquitin ligase complex, catalyzing the covalent attachment of ubiquitin moieties onto substrate proteins, such as BCL2, SYT11, CCNE1, GPR37, RHOT1/MIRO1, MFN1, MFN2, STUB1, SNCAIP, SEPT5, TOMM20, USP30, ZNF746 and AIMP2. It mediates monoubiquitination as well as Lys-6-, Lys-11-, Lys-48- and Lys-63-linked polyubiquitination of substrates depending on the context. Parkin may enhance cell viability and protects dopaminergic neurons from oxidative stress-mediated death by regulating mitochondrial function. It also limits the production of reactive oxygen species (ROS), and regulates cyclin-E during neuronal apoptosis. Moreover, parkin displays a ubiquitin ligase-independent function in transcriptional repression of p53. Parkin contains an N-terminal ubiquitin-like (Ubl) domain and a C-terminal RBR domain that was previously known as RING-BetweenRING-RING domain or TRIAD [two RING fingers and a DRIL (double RING finger linked)] domain. Based on current understanding of the structural biology of RBR ligases, the nomenclature of RBR has been corrected as RING-BRcat (benign-catalytic)-Rcat (required-for-catalysis) recently. The RBR (RING1-BRcat-Rcat) domain use an auto-inhibitory mechanism to modulate ubiquitination activity, as well as a hybrid mechanism that combines aspects from both RING and HECT E3 ligase function to facilitate the ubiquitination reaction.


Pssm-ID: 340496  Cd Length: 74  Bit Score: 36.89  E-value: 3.58e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 124430766   3 IQVRTiDGSQTRTIEdVSRKATIEELRERVWALFDVRPECQRLFYRGKQLENGYTLFDYDVGLNDIIQLLVRP 75
Cdd:cd01798    1 VFVRF-NSSHGFPVE-VDSDWSILQLKEVVAKRQGVPPDQLRIIFAGKELSDDLTLQNCDLGQQSIVHAVQGP 71
RING-HC_RNF8 cd16535
RING finger, HC subclass, found in RING finger protein 8 (RNF8) and similar proteins; RNF8 is ...
734-785 3.76e-03

RING finger, HC subclass, found in RING finger protein 8 (RNF8) and similar proteins; RNF8 is a telomere-associated E3 ubiquitin-protein ligase that plays an important role in DNA double-strand break (DSB) repair via histone ubiquitination. It is localized in the nucleus and interacts with class III E2s (UBE2E2, UbcH6, and UBE2E3), but not with other E2s (UbcH5, UbcH7, UbcH10, hCdc34, and hBendless). It recruits UBC13 for lysine 63-based self polyubiquitylation. Its deficiency causes neuronal pathology and cognitive decline, and its loss results in neuron degeneration. RNF8, together with RNF168, catalyzes a series of ubiquitylation events on substrates such as H2A and H2AX, with the H2AK13/15 ubiquitylation being particularly important for recruitment of repair factors p53-binding protein 1 (53BP1) or the RAP80-BRCA1 complex to sites of DSBs. RNF8 mediates the ubiquitination of gammaH2AX, and recruits 53BP1 and BRCA1 to DNA damage sites which promotes DNA damage response (DDR) and inhibits chromosomal instability. Moreover, RNF8 interacts with retinoid X receptor alpha (RXR alpha) and enhances its transcription-stimulating activity. It also regulates the rate of exit from mitosis and cytokinesis. RNF8 contains an N-terminal forkhead-associated (FHA) domain and a C-terminal C3HC4-type RING-HC finger.


Pssm-ID: 438197 [Multi-domain]  Cd Length: 64  Bit Score: 36.60  E-value: 3.76e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 124430766 734 CVCCQELVYQPVTTECFHNVCKDCLqRSFKAQVFSCPACRHDL-GQNYVMVLN 785
Cdd:cd16535    4 CSICSELFIEAVTLNCSHSFCSYCI-TEWMKRKKECPICRKPItSKTRSLVLD 55
RING-HC_Bre1-like cd16499
RING finger, HC subclass, found in yeast Bre1 and its homologs from eukaryotes; Bre1 is an E3 ...
726-782 3.76e-03

RING finger, HC subclass, found in yeast Bre1 and its homologs from eukaryotes; Bre1 is an E3 ubiquitin-protein ligase that catalyzes monoubiquitination of histone H2B in concert with the E2 ubiquitin-conjugating enzyme, Rad6. The Rad6-Bre1-mediated histone H2B ubiquitylation modulates the formation of double-strand breaks (DSBs) during meiosis in yeast. it is also required, indirectly, for the methylation of histone 3 on lysine 4 (H3K4) and 79. RNF20, also known as BRE1A and RNF40, also known as BRE1B, are the mammalian homologs of Bre1. They work together to form a heterodimeric Bre1 complex that facilitate the K120 monoubiquitination of histone H2B (H2Bub1), a DNA damage-induced histone modification that is crucial for recruitment of the chromatin remodeler SNF2h to DNA double-strand break (DSB) damage sites. Moreover, the Bre1 complex acts as a tumor suppressor, augmenting expression of select tumor suppressor genes and suppressing select oncogenes. Deficiency in the mammalian histone H2B ubiquitin ligase Bre1 leads to replication stress and chromosomal instability. All subfamily members contain a C3HC4-type RING-HC finger at its C-terminus.


Pssm-ID: 438162 [Multi-domain]  Cd Length: 59  Bit Score: 36.38  E-value: 3.76e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 124430766 726 KKLEQSFMCVCCQELVYQPVTTECFHNVCKDCLQRSFKAQVFSCPACRHDLGQNYVM 782
Cdd:cd16499    1 KDLRELLKCSVCNDRFKDVIITKCGHVFCNECVQKRLETRQRKCPGCGKAFGANDVQ 57
RING-HC_RNF213 cd16561
RING finger, HC subclass, found in RING finger protein 213 (RNF213) and similar proteins; ...
733-779 3.79e-03

RING finger, HC subclass, found in RING finger protein 213 (RNF213) and similar proteins; RNF213, also known as ALK lymphoma oligomerization partner on chromosome 17 or Moyamoya steno-occlusive disease-associated AAA+ and RING finger protein (mysterin), is an intracellular soluble protein that functions as an E3 ubiquitin-protein ligase and AAA+ ATPase, which possibly contributes to vascular development through mechanical processes in the cell. It plays a unique role in endothelial cells for proper gene expression in response to inflammatory signals from the environment. Mutations in RNF213 may be associated with Moyamoya disease (MMD), an idiopathic cerebrovascular occlusive disorder prevalent in East Asia. It also acts as a nuclear marker for acanthomorph phylogeny. RNF213 contains two tandem enzymatically active AAA+ ATPase modules and a C3HC4-type RING-HC finger. It can form a huge ring-shaped oligomeric complex.


Pssm-ID: 438223 [Multi-domain]  Cd Length: 50  Bit Score: 36.10  E-value: 3.79e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 124430766 733 MCVCCQELVYQPVTTECFHNVCKDCLQRSFKAQVfSCPACRHDLGQN 779
Cdd:cd16561    4 ECSICLEDLNDPVKLPCDHVFCEECIRQWLPGQM-SCPLCRTELPDD 49
RING-HC_GEFO-like cd16507
RING finger, HC subclass, found in Dictyostelium discoideum Ras guanine nucleotide exchange ...
724-773 4.40e-03

RING finger, HC subclass, found in Dictyostelium discoideum Ras guanine nucleotide exchange factor O (RasGEFO) and similar proteins; RasGEFO, also known as RasGEF domain-containing protein O, functions as a Ras guanine-nucleotide exchange factor (RasGEFs), activating Ras by catalyzing the replacement of GDP with GTP. RasGEFs are particularly important for signaling in development and chemotaxis in many organisms, including Dictyostelium. RasGEFO contains a C3HC4-type RING-HC finger that may be responsible for E3 ubiquitin ligase activity.


Pssm-ID: 438170 [Multi-domain]  Cd Length: 58  Bit Score: 36.17  E-value: 4.40e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 124430766 724 FLKKLEQSFMCVCCQELVYQP-VTTECFHNVCKDCLQRSFKAQvfSCPACR 773
Cdd:cd16507    2 KSLNLLQSLTCGICQNLFKDPnTLIPCGHAFCLDCLTTNASIK--NCIQCK 50
RING-HC_TRIM56_C-V cd16584
RING finger, HC subclass, found in tripartite motif-containing protein 56 (TRIM56) and similar ...
734-776 4.47e-03

RING finger, HC subclass, found in tripartite motif-containing protein 56 (TRIM56) and similar proteins; TRIM56, also known as RING finger protein 109 (RNF109), is a virus-inducible E3 ubiquitin ligase that restricts pestivirus infection. It positively regulates the Toll-like receptor 3 (TLR3) antiviral signaling pathway, and possesses antiviral activity against bovine viral diarrhea virus (BVDV), a ruminant pestivirus classified within the family Flaviviridae shared by tick-borne encephalitis virus (TBEV). It also possesses antiviral activity against two classical flaviviruses, yellow fever virus (YFV) and dengue virus (DENV), as well as a human coronavirus, HCoV-OC43, which is responsible for a significant share of common cold cases. It may not act on positive-strand RNA viruses indiscriminately. Moreover, TRIM56 is an interferon-inducible E3 ubiquitin ligase that modulates STING to confer double-stranded DNA-mediated innate immune responses. TRIM56 belongs to the C-V subclass of the TRIM (tripartite motif) family of proteins that are defined by an N-terminal RBCC (RING, Bbox, and coiled coil) domain, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as an uncharacterized region positioned C-terminal to the RBCC domain.


Pssm-ID: 438246 [Multi-domain]  Cd Length: 56  Bit Score: 36.12  E-value: 4.47e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 124430766 734 CVCCQELVYQPVTTECFHNVCKDCLQRSFKAQVFSCPACRHDL 776
Cdd:cd16584    4 CKICLEQLRAPKTLPCLHTYCQDCLAQLADGGRVRCPECRETV 46
PHD_BRPF cd15572
PHD finger found in bromodomain and PHD finger-containing (BRPF) proteins; The family of BRPF ...
340-393 5.01e-03

PHD finger found in bromodomain and PHD finger-containing (BRPF) proteins; The family of BRPF proteins includes BRPF1, BRD1/BRPF2, and BRPF3. They 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. This model corresponds to the canonical Cys4HisCys3 PHD finger.


Pssm-ID: 277047 [Multi-domain]  Cd Length: 54  Bit Score: 35.67  E-value: 5.01e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 124430766 340 DKTChmCSCHKcGEKRDPNMQLLCDECNMAYHIYCLSPPLdkVPEEEyWYCPSC 393
Cdd:cd15572    1 DAVC--CICLD-GECQNSNVILFCDMCNLAVHQECYGVPY--IPEGQ-WLCRRC 48
BAH_plant_2 cd04718
BAH, or Bromo Adjacent Homology domain, plant-specific sub-family with unknown function. BAH ...
370-413 5.46e-03

BAH, or Bromo Adjacent Homology domain, plant-specific sub-family with unknown function. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.


Pssm-ID: 240069  Cd Length: 148  Bit Score: 37.95  E-value: 5.46e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 124430766 370 YHIYCLSPPLDKVPEEEyWYCPSCKTDSSEVVKAGERLKLSKKK 413
Cdd:cd04718    2 FHLCCLRPPLKEVPEGD-WICPFCEVEKSGQSAMPQLPPTSRSA 44
RING-HC_TRIM31_C-V cd16582
RING finger, HC subclass, found in tripartite motif-containing protein 31 (TRIM31) and similar ...
734-772 5.75e-03

RING finger, HC subclass, found in tripartite motif-containing protein 31 (TRIM31) and similar proteins; TRIM31 is an E3 ubiquitin-protein ligase that primarily localizes to the cytoplasm, but is also associated with the mitochondria. It can negatively regulate cell proliferation and may be a potential biomarker of gastric cancer as it is overexpressed from the early stage of gastric carcinogenesis. TRIM31 is downregulated in non-small cell lung cancer and serves as a potential tumor suppressor. It interacts with p52 (Shc) and inhibits Src-induced anchorage-independent growth. TRIM31 belongs to the C-V subclass of the TRIM (tripartite motif) family of proteins that are defined by an N-terminal RBCC (RING, Bbox, and coiled coil) domain, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as an uncharacterized region positioned C-terminal to the RBCC domain.


Pssm-ID: 438244 [Multi-domain]  Cd Length: 44  Bit Score: 35.19  E-value: 5.75e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 124430766 734 CVCCQELVYQPVTTECFHNVCKDCLQRSFK--AQVFSCPAC 772
Cdd:cd16582    4 CPICLDILQKPVTIDCGHNFCLQCITQIGEtsCGFFKCPLC 44
mRING-HC-C4C4_TRIM37_C-VIII cd16619
Modified RING finger, HC subclass (C4C4-type), found in tripartite motif-containing protein 37 ...
732-773 5.75e-03

Modified RING finger, HC subclass (C4C4-type), found in tripartite motif-containing protein 37 (TRIM37) and similar proteins; TRIM37, also known as mulibrey nanism protein, or MUL, is a peroxisomal E3 ubiquitin-protein ligase that is involved in the tumorigenesis of several cancer types, including pancreatic ductal adenocarcinoma (PDAC), hepatocellular carcinoma (HCC), breast cancer, and sporadic fibrothecoma. It mono-ubiquitinates histone H2A, a chromatin modification associated with transcriptional repression. Moreover, TRIM37 possesses anti-HIV-1 activity, and interferes with viral DNA synthesis. Mutations in the human TRIM37 gene (also known as MUL) cause Mulibrey (muscle-liver-brain-eye) nanism, a rare growth disorder of prenatal onset characterized by dysmorphic features, pericardial constriction, and hepatomegaly. TRIM37 belongs to the C-VIII subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C4C4-type RING finger, whose overall folding is similar to that of the typical C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a MATH (meprin and TRAF-C homology) domain positioned C-terminal to the RBCC domain. Its MATH domain has been shown to interact with the TRAF (TNF-Receptor-Associated Factor) domain of six known TRAFs in vitro.


Pssm-ID: 438281 [Multi-domain]  Cd Length: 43  Bit Score: 35.41  E-value: 5.75e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 124430766 732 FMCVCCQELVYQPVT-TECFHNVCKDCLQRSFKAQVFSCPACR 773
Cdd:cd16619    1 FRCFICMEKLRDPRLcPHCSKLFCKGCIRRWLSEQRSSCPHCR 43
mRING-HC-C3HC3D_TRAF6 cd16643
Modified RING finger, HC subclass (C3HC3D-type), found in tumor necrosis factor (TNF) ...
732-770 6.21e-03

Modified RING finger, HC subclass (C3HC3D-type), found in tumor necrosis factor (TNF) receptor-associated factor 6 (TRAF6) and similar proteins; TRAF6, also known as interleukin-1 signal transducer or RING finger protein 85 (RNF85), is a cytoplasmic adapter protein that mediates signals induced by the tumor necrosis factor receptor (TNFR) superfamily and Toll-like receptor (TLR)/interleukin-1 receptor (IL-1R) family. It functions as a mediator involved in the activation of mitogen-activated protein kinase (MAPK), phosphoinositide 3-kinase (PI3K), and interferon regulatory factor pathways, as well as in IL-1R-mediated activation of NF-kappaB. TRAF6 is also an oncogene that plays a vital role in K-RAS-mediated oncogenesis. TRAF6 contains an N-terminal domain with a modified C3HC3D-type RING-HC finger and several zinc fingers, and a C-terminal TRAF domain that comprises a coiled coil domain and a conserved TRAF-C domain.


Pssm-ID: 438305 [Multi-domain]  Cd Length: 58  Bit Score: 35.82  E-value: 6.21e-03
                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 124430766 732 FMCVCCQELVYQPVTTECFHNVCKDCLQRSFKAQVFSCP 770
Cdd:cd16643    2 YECPICLMALREPVQTPCGHRFCKACILKSIREAGHKCP 40
PHD_TAF3 cd15522
PHD finger found in transcription initiation factor TFIID subunit 3 (TAF3); TAF3 (also termed ...
348-393 7.66e-03

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: 34.96  E-value: 7.66e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 124430766 348 CHKCGEKRDPNMQLLCDECNMAYHIYCLSppLDKVP-EEEYWYCPSC 393
Cdd:cd15522    2 CPICKKPDDGSPMIGCDECDDWYHWECVG--ITDEPpEEDDWFCPKC 46
PHD_PRKCBP1 cd15538
PHD finger found in protein kinase C-binding protein 1 (PRKCBP1); PRKCBP1, also termed ...
348-393 7.84e-03

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: 34.99  E-value: 7.84e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 124430766 348 CHKCGEkrdpnmQLLCDECNMAYHIYCLSPPldkVPEEEYWYCPSC 393
Cdd:cd15538    5 CHKEGQ------VLCCSLCPRVYHKKCLKLT---SEPDEDWVCPEC 41
RING-HC_HLTF cd16509
RING finger, HC subclass, found in helicase-like transcription factor (HLTF) and similar ...
734-776 8.23e-03

RING finger, HC subclass, found in helicase-like transcription factor (HLTF) and similar proteins; HLTF, also known as DNA-binding protein/plasminogen activator inhibitor 1 regulator, HIP116, RING finger protein 80, SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 3, or sucrose nonfermenting protein 2-like 3, is a yeast RAD5 homolog found in mammals. It has both E3 ubiquitin ligase and DNA helicase activities, and plays a pivotal role in the template-switching pathway of DNA damage tolerance. It is involved in Lys-63-linked poly-ubiquitination of proliferating cell nuclear antigen (PCNA) at Lys-164 and in the regulation of DNA damage tolerance. It shows double-stranded DNA translocase activity with 3'-5' polarity, thereby facilitating regression of the replication fork. HLTF contains an N-terminal HIRAN (HIP116 and RAD5 N-terminal) domain, a SWI/SNF helicase domain that is divided into N- and C-terminal parts by an insertion of a C3HC4-type RING-HC finger involved in the poly-ubiquitination of PCNA.


Pssm-ID: 438172 [Multi-domain]  Cd Length: 53  Bit Score: 34.97  E-value: 8.23e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 124430766 734 CVCCQELVYQPVTTECFHNVCKDCLQRSFKAQVFSCPACRHDL 776
Cdd:cd16509    6 CAICLDSLTNPVITPCAHVFCRRCICEVIQREKAKCPMCRAPL 48
zf-C3HC4_3 pfam13920
Zinc finger, C3HC4 type (RING finger);
733-773 8.78e-03

Zinc finger, C3HC4 type (RING finger);


Pssm-ID: 433580 [Multi-domain]  Cd Length: 50  Bit Score: 35.04  E-value: 8.78e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 124430766  733 MCVCCQELVYQPVTTECFHNV-CKDCLQRsFKAQVFSCPACR 773
Cdd:pfam13920   4 LCVICLDRPRNVVLLPCGHLClCEECAER-LLRKKKKCPICR 44
RING-HC_PML_C-V cd16579
RING finger, HC subclass, found in promyelocytic leukemia protein (PML) and similar proteins; ...
729-773 8.80e-03

RING finger, HC subclass, found in promyelocytic leukemia protein (PML) and similar proteins; Protein PML, also known as RING finger protein 71 (RNF71) or tripartite motif-containing protein 19 (TRIM19), is predominantly a nuclear protein with a broad intrinsic antiviral activity. It is the eponymous component of PML nuclear bodies (PML NBs) and has been implicated in a wide variety of cell processes, including DNA damage signaling, apoptosis, and transcription. PML interferes with the replication of many unrelated viruses, including human immunodeficiency virus 1 (HIV-1), human foamy virus (HFV), poliovirus, influenza virus, rabies virus, EMCV, adeno-associated virus (AAV), and vesicular stomatitis virus (VSV). It also selectively interacts with misfolded proteins through distinct substrate recognition sites and conjugates these proteins with the small ubiquitin-like modifiers (SUMOs) through its SUMO ligase activity. PML belongs to the C-V subclass of the TRIM (tripartite motif) family of proteins that are defined by an N-terminal RBCC (RING, Bbox, and coiled coil) domain, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as an uncharacterized region positioned C-terminal to the RBCC domain.


Pssm-ID: 438241 [Multi-domain]  Cd Length: 52  Bit Score: 35.22  E-value: 8.80e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 124430766 729 EQSFMCVCCQELVYQPVTTECFHNVCKDCLQRS----FKAQVFSCPACR 773
Cdd:cd16579    2 FKFLRCPGCKAEYKCPKLLPCLHTVCSGCLEALaeqaSETTEFQCPICK 50
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.20
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.
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