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Conserved domains on  [gi|341941803|sp|P15919|]
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RecName: Full=V(D)J recombination-activating protein 1; Short=RAG-1; Includes: RecName: Full=Endonuclease RAG1; Includes: RecName: Full=E3 ubiquitin-protein ligase RAG1; AltName: Full=RING-type E3 ubiquitin transferase RAG1

Protein Classification

V(D)J recombination-activating protein 1( domain architecture ID 12117148)

recombination activating protein 1, also known as V(D)J recombination-activating protein 1, endonuclease RAG1, or E3 ubiquitin-protein ligase RAG1, is the catalytic component of the RAG complex, a multiprotein complex that mediates the DNA cleavage phase during V(D)J recombination

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
RAG1 super family cl20149
Recombination-activation protein 1 (RAG1), recombinase; This family is one of the two ...
386-1024 0e+00

Recombination-activation protein 1 (RAG1), recombinase; This family is one of the two different components of the RAG1-RAG2 V(D)J recombinase complex. The RAG complex, consisting of two RAG1 and two RAG2 proteins is a multi-protein complex that mediates DNA cleavage during V(D)J (variable-diversity-joining) recombination. RAG1 mediates DNA-binding to the conserved recombination signal sequences (RSS). Many of the proteins in this family are fragments. Solution of the structure of the complex of RAG1 and RAG2 shows that each protein dimerizes with itself and each pair then complexes together to from the RAG1-RAG2 V(D)J recombinase enzyme. The different structural elements in RAG1 for UniProtKB:P15919 are: an N-terminal nonamer-binding domain from residues 391-459; a dimerization and DNA-binding domain from 459-515; an extended pre-RNase H domain from 515-588; the catalytic RNase H domain from 588-719; a ZnC2 domain from 719-791; and ZnH2 domain from 791-962; and a three-helix C-terminal domain from 962-1008.


The actual alignment was detected with superfamily member pfam12940:

Pssm-ID: 315595  Cd Length: 653  Bit Score: 1155.18  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 341941803   386 INKGGRPRQHLLSLTRRAQKHRLRELKIQVKEFADKEEGGDVKAVCLTLFLLALRARNEHRQADELEAIMQGRGSGLQPA 465
Cdd:pfam12940    6 TNKGGRPRQHLLSLTRRAQKHRLRDLKHQVKVFADKEEGGDIKSVCLTLFLLALRAGNEHRQADELEAMMQGRGFGLHPA 85
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 341941803   466 VCLAIRVNTFLSCSQYHKMYRTVKAITGRQIFQPLHALRNAEKVLLPGYHPFEWQPPLKNVSSRTDVGIIDGLSGLASSV 545
Cdd:pfam12940   86 VCLAIRVNTFLSCSQYHKMYRTVKATSGRQIFQPLHTLRAAEKALLPGFHHFEWQPALKNVSPSCDVGIIDGLSGWSPSV 165
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 341941803   546 DEYPVDTIAKRFRYDSALVSALMDMEEDILEGMRSQDLDDY-LNGPFTVVVKESCDGMGDVSEKHGSGPAVPEKAVRFSF 624
Cdd:pfam12940  166 DDQPADTITRRFRYDVALVAALKDLEEDILEGLKEQGLDDSaCTEGFSVMIKECCDGMGDVSEKHGGGPAVPEKAVRFSF 245
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 341941803   625 TVMRITI---EHGSQNVKVFEEPKPNSELCCKPLCLMLADESDHETLTAILSPLIAEREAMKSSELTLEMGGIPRTFKFI 701
Cdd:pfam12940  246 TIMSVSIladDEEGEEVAIFHELKPNSELCCKPLCLMFADESDHETLTAILAPIMAEREAMKESRLILSIGGLLRSFRFH 325
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 341941803   702 FRGTGYDEKLVREVEGLEASGSVYICTLCDTTRLEASQNLVFHSITRSHAENLQRYEVWRSNPYHESVEELRDRVKGVSA 781
Cdd:pfam12940  326 FRGTGYDEKLVRDMEGLEASGSTYICTLCDSSRAEASKNKVLHAITRSHEENLERYEIWRTNPFSESADDLRDRVKGISA 405
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 341941803   782 KPFIETVPSIDALHCDIGNAAEFYKIFQLEIGEVYKHPNASKEERKRWQATLDKHLRKRMNLKPIMRMNGNFARKLMTQE 861
Cdd:pfam12940  406 KPFLETQACIDALHCDIGNATEFYKIFQDEIGEVHKKANPSKEERKRWQAALDKQLRKKMKLKPVMRMNGNFARKLMTQE 485
                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 341941803   862 TVDAVCELIPSEERHEALRELMDLYLKMKPVWRSSCPAKECPESLCQYSFNSQRFAELLSTKFKYRYEGKITNYFHKTLA 941
Cdd:pfam12940  486 AVDAVCELVPSEERQEALRELMHLYLQMKPVWRATCPAKECPDLLCRYSFNSQRFADLLSTTFKYRYDGKITNYLHKTLA 565
                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 341941803   942 HVPEIIERDGSIGAWASEGNESGNKLFRRFRKMNARQSKCYEMEDVLKHHWLYTSKYLQKFMNAH-NALKSSGFTMNSKE 1020
Cdd:pfam12940  566 HVPEIIERDGSIGAWASEGNESANKLFRRFRKMNARQSKSFELEDILKHHWLYTSKYLQKFMEAHkDSAKALEATIDPVE 645

                   ....
gi 341941803  1021 TLGD 1024
Cdd:pfam12940  646 IQDD 649
RAG1_imp_bd pfam12560
RAG1 importin binding; This region of RAG1 is responsible for binding to importin alpha.
12-287 1.70e-129

RAG1 importin binding; This region of RAG1 is responsible for binding to importin alpha.


:

Pssm-ID: 432636  Cd Length: 282  Bit Score: 393.70  E-value: 1.70e-129
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 341941803    12 SSAPDEIQHPQIKFSEWKFKLFRVRSFEKAPEEAQK-EKDSSEGKPYLEQSPVVP-EKPGGQNSILTQRALKLHPKFSKK 89
Cdd:pfam12560    1 SSMPDELQHPYKKFSEWKFKLFRVRSFEKAPLESETtEKGVALGLSSPEAPPTELgDGTAPGGSVLTLCGGKKKKEVVEK 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 341941803    90 FHADGKSSDKAVHQARLRHFCRICGNRFKSdGHSRRYPVHGPVDAKTQSLFRKKEKRVTSWPDLIARIFRIDVKADVDSI 169
Cdd:pfam12560   81 RRDDGKQQEKATHQALLRLLCRICGMSLKT-KKGRRHPVHGPVDDSTKCLLRKKEKKATSWPDLILKVFKVDVKGDVDSI 159
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 341941803   170 HPTEFCHDCWSIMHRkfssSHSQVYFPRKVTVEWHPHTPSCDICFTAHRGLKRKRHQPNVQLSKKLKTVLNHARRDRRKR 249
Cdd:pfam12560  160 HPTFFCHRCWTVIRR----GGGECSFPRTRVPEWKPHSSSCDLCPTKRRGLKRKGLPPNLQLAKRLKTDSDRARRGRRRK 235
                          250       260       270       280
                   ....*....|....*....|....*....|....*....|....*..
gi 341941803   250 ---------TQARVSSKEVLKKISNCSKIHLSTKLLAVDFPAHFVKS 287
Cdd:pfam12560  236 qwrsaitwwKQAAIQRKWVVKKITNCKKIHLSTKLLAVDYPVDFVKS 282
RING-HC_RAG1 cd16530
RING finger, HC subclass, found in recombination activating gene-1 (RAG-1) and similar ...
286-331 9.37e-27

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: 103.29  E-value: 9.37e-27
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 341941803  286 KSISCQICEHILADPVETSCKHLFCRICILRCLKVMGSYCPSCRYP 331
Cdd:cd16530     1 KSVSCQVCEHILADPVQTPCKHLFCRTCILKCLKVMGSYCPSCRYP 46
zf-RAG1 pfam10426
Recombination-activating protein 1 zinc-finger domain; This is a C2-H2 zinc-finger domain ...
351-380 7.03e-11

Recombination-activating protein 1 zinc-finger domain; This is a C2-H2 zinc-finger domain closely resembling the classical TFIIIA-type zinc-finger, CX3FX5LX2-3H, despite having a valine and a tyrosine at the core instead of a phenylalanine and a leucine, hence CX3VX1LX2YX2H. The structure, nevertheless, contains the characteristic two-stranded beta-sheet and alpha-helix of a classical zinc-finger. The domain binds one zinc and, in complex with the zinc-RING-finger domain, helps to stabilize the whole of the dimerization region of recombination activating protein 1 (RAG1). The function of the whole is to bind double-stranded DNA.


:

Pssm-ID: 431278  Cd Length: 30  Bit Score: 57.52  E-value: 7.03e-11
                           10        20        30
                   ....*....|....*....|....*....|
gi 341941803   351 LMVKCPAQDCNEEVSLEKYNHHVSSHKESK 380
Cdd:pfam10426    1 LVIRCPAKDCDEEVRLEKYGQHLSSHKEGK 30
 
Name Accession Description Interval E-value
RAG1 pfam12940
Recombination-activation protein 1 (RAG1), recombinase; This family is one of the two ...
386-1024 0e+00

Recombination-activation protein 1 (RAG1), recombinase; This family is one of the two different components of the RAG1-RAG2 V(D)J recombinase complex. The RAG complex, consisting of two RAG1 and two RAG2 proteins is a multi-protein complex that mediates DNA cleavage during V(D)J (variable-diversity-joining) recombination. RAG1 mediates DNA-binding to the conserved recombination signal sequences (RSS). Many of the proteins in this family are fragments. Solution of the structure of the complex of RAG1 and RAG2 shows that each protein dimerizes with itself and each pair then complexes together to from the RAG1-RAG2 V(D)J recombinase enzyme. The different structural elements in RAG1 for UniProtKB:P15919 are: an N-terminal nonamer-binding domain from residues 391-459; a dimerization and DNA-binding domain from 459-515; an extended pre-RNase H domain from 515-588; the catalytic RNase H domain from 588-719; a ZnC2 domain from 719-791; and ZnH2 domain from 791-962; and a three-helix C-terminal domain from 962-1008.


Pssm-ID: 315595  Cd Length: 653  Bit Score: 1155.18  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 341941803   386 INKGGRPRQHLLSLTRRAQKHRLRELKIQVKEFADKEEGGDVKAVCLTLFLLALRARNEHRQADELEAIMQGRGSGLQPA 465
Cdd:pfam12940    6 TNKGGRPRQHLLSLTRRAQKHRLRDLKHQVKVFADKEEGGDIKSVCLTLFLLALRAGNEHRQADELEAMMQGRGFGLHPA 85
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 341941803   466 VCLAIRVNTFLSCSQYHKMYRTVKAITGRQIFQPLHALRNAEKVLLPGYHPFEWQPPLKNVSSRTDVGIIDGLSGLASSV 545
Cdd:pfam12940   86 VCLAIRVNTFLSCSQYHKMYRTVKATSGRQIFQPLHTLRAAEKALLPGFHHFEWQPALKNVSPSCDVGIIDGLSGWSPSV 165
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 341941803   546 DEYPVDTIAKRFRYDSALVSALMDMEEDILEGMRSQDLDDY-LNGPFTVVVKESCDGMGDVSEKHGSGPAVPEKAVRFSF 624
Cdd:pfam12940  166 DDQPADTITRRFRYDVALVAALKDLEEDILEGLKEQGLDDSaCTEGFSVMIKECCDGMGDVSEKHGGGPAVPEKAVRFSF 245
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 341941803   625 TVMRITI---EHGSQNVKVFEEPKPNSELCCKPLCLMLADESDHETLTAILSPLIAEREAMKSSELTLEMGGIPRTFKFI 701
Cdd:pfam12940  246 TIMSVSIladDEEGEEVAIFHELKPNSELCCKPLCLMFADESDHETLTAILAPIMAEREAMKESRLILSIGGLLRSFRFH 325
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 341941803   702 FRGTGYDEKLVREVEGLEASGSVYICTLCDTTRLEASQNLVFHSITRSHAENLQRYEVWRSNPYHESVEELRDRVKGVSA 781
Cdd:pfam12940  326 FRGTGYDEKLVRDMEGLEASGSTYICTLCDSSRAEASKNKVLHAITRSHEENLERYEIWRTNPFSESADDLRDRVKGISA 405
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 341941803   782 KPFIETVPSIDALHCDIGNAAEFYKIFQLEIGEVYKHPNASKEERKRWQATLDKHLRKRMNLKPIMRMNGNFARKLMTQE 861
Cdd:pfam12940  406 KPFLETQACIDALHCDIGNATEFYKIFQDEIGEVHKKANPSKEERKRWQAALDKQLRKKMKLKPVMRMNGNFARKLMTQE 485
                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 341941803   862 TVDAVCELIPSEERHEALRELMDLYLKMKPVWRSSCPAKECPESLCQYSFNSQRFAELLSTKFKYRYEGKITNYFHKTLA 941
Cdd:pfam12940  486 AVDAVCELVPSEERQEALRELMHLYLQMKPVWRATCPAKECPDLLCRYSFNSQRFADLLSTTFKYRYDGKITNYLHKTLA 565
                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 341941803   942 HVPEIIERDGSIGAWASEGNESGNKLFRRFRKMNARQSKCYEMEDVLKHHWLYTSKYLQKFMNAH-NALKSSGFTMNSKE 1020
Cdd:pfam12940  566 HVPEIIERDGSIGAWASEGNESANKLFRRFRKMNARQSKSFELEDILKHHWLYTSKYLQKFMEAHkDSAKALEATIDPVE 645

                   ....
gi 341941803  1021 TLGD 1024
Cdd:pfam12940  646 IQDD 649
RAG1_imp_bd pfam12560
RAG1 importin binding; This region of RAG1 is responsible for binding to importin alpha.
12-287 1.70e-129

RAG1 importin binding; This region of RAG1 is responsible for binding to importin alpha.


Pssm-ID: 432636  Cd Length: 282  Bit Score: 393.70  E-value: 1.70e-129
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 341941803    12 SSAPDEIQHPQIKFSEWKFKLFRVRSFEKAPEEAQK-EKDSSEGKPYLEQSPVVP-EKPGGQNSILTQRALKLHPKFSKK 89
Cdd:pfam12560    1 SSMPDELQHPYKKFSEWKFKLFRVRSFEKAPLESETtEKGVALGLSSPEAPPTELgDGTAPGGSVLTLCGGKKKKEVVEK 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 341941803    90 FHADGKSSDKAVHQARLRHFCRICGNRFKSdGHSRRYPVHGPVDAKTQSLFRKKEKRVTSWPDLIARIFRIDVKADVDSI 169
Cdd:pfam12560   81 RRDDGKQQEKATHQALLRLLCRICGMSLKT-KKGRRHPVHGPVDDSTKCLLRKKEKKATSWPDLILKVFKVDVKGDVDSI 159
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 341941803   170 HPTEFCHDCWSIMHRkfssSHSQVYFPRKVTVEWHPHTPSCDICFTAHRGLKRKRHQPNVQLSKKLKTVLNHARRDRRKR 249
Cdd:pfam12560  160 HPTFFCHRCWTVIRR----GGGECSFPRTRVPEWKPHSSSCDLCPTKRRGLKRKGLPPNLQLAKRLKTDSDRARRGRRRK 235
                          250       260       270       280
                   ....*....|....*....|....*....|....*....|....*..
gi 341941803   250 ---------TQARVSSKEVLKKISNCSKIHLSTKLLAVDFPAHFVKS 287
Cdd:pfam12560  236 qwrsaitwwKQAAIQRKWVVKKITNCKKIHLSTKLLAVDYPVDFVKS 282
RING-HC_RAG1 cd16530
RING finger, HC subclass, found in recombination activating gene-1 (RAG-1) and similar ...
286-331 9.37e-27

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: 103.29  E-value: 9.37e-27
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 341941803  286 KSISCQICEHILADPVETSCKHLFCRICILRCLKVMGSYCPSCRYP 331
Cdd:cd16530     1 KSVSCQVCEHILADPVQTPCKHLFCRTCILKCLKVMGSYCPSCRYP 46
zf-RAG1 pfam10426
Recombination-activating protein 1 zinc-finger domain; This is a C2-H2 zinc-finger domain ...
351-380 7.03e-11

Recombination-activating protein 1 zinc-finger domain; This is a C2-H2 zinc-finger domain closely resembling the classical TFIIIA-type zinc-finger, CX3FX5LX2-3H, despite having a valine and a tyrosine at the core instead of a phenylalanine and a leucine, hence CX3VX1LX2YX2H. The structure, nevertheless, contains the characteristic two-stranded beta-sheet and alpha-helix of a classical zinc-finger. The domain binds one zinc and, in complex with the zinc-RING-finger domain, helps to stabilize the whole of the dimerization region of recombination activating protein 1 (RAG1). The function of the whole is to bind double-stranded DNA.


Pssm-ID: 431278  Cd Length: 30  Bit Score: 57.52  E-value: 7.03e-11
                           10        20        30
                   ....*....|....*....|....*....|
gi 341941803   351 LMVKCPAQDCNEEVSLEKYNHHVSSHKESK 380
Cdd:pfam10426    1 LVIRCPAKDCDEEVRLEKYGQHLSSHKEGK 30
zf-C3HC4 pfam00097
Zinc finger, C3HC4 type (RING finger); The C3HC4 type zinc-finger (RING finger) is a ...
290-328 2.05e-09

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: 53.90  E-value: 2.05e-09
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|
gi 341941803   290 CQICEHILADPVETS-CKHLFCRICILRCLKVMGSYCPSC 328
Cdd:pfam00097    1 CPICLEEPKDPVTLLpCGHLFCSKCIRSWLESGNVTCPLC 40
rad18 TIGR00599
DNA repair protein rad18; All proteins in this family for which functions are known are ...
287-364 7.57e-09

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: 58.86  E-value: 7.57e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 341941803   287 SISCQICEHILADPVETSCKHLFCRICILRCLKVMGSyCPSCRYPCFPTDL------ESPVKSFLNILNSLM----VKCP 356
Cdd:TIGR00599   26 SLRCHICKDFFDVPVLTSCSHTFCSLCIRRCLSNQPK-CPLCRAEDQESKLrsnwlvSEIVESFKNLRPSLLeflrIPKT 104

                   ....*...
gi 341941803   357 AQDCNEEV 364
Cdd:TIGR00599  105 TPVENPDL 112
RING smart00184
Ring finger; E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and ...
290-328 1.85e-07

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: 48.27  E-value: 1.85e-07
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|
gi 341941803    290 CQIC-EHILADPVETSCKHLFCRICILRCLKVMGSYCPSC 328
Cdd:smart00184    1 CPIClEEYLKDPVILPCGHTFCRSCIRKWLESGNNTCPIC 40
RAD18 COG5432
RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms];
287-331 1.04e-05

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


Pssm-ID: 227719 [Multi-domain]  Cd Length: 391  Bit Score: 48.93  E-value: 1.04e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 341941803  287 SISCQICEHILADPVETSCKHLFCRICILRCLKVMgSYCPSCRYP 331
Cdd:COG5432    25 MLRCRICDCRISIPCETTCGHTFCSLCIRRHLGTQ-PFCPVCRED 68
 
Name Accession Description Interval E-value
RAG1 pfam12940
Recombination-activation protein 1 (RAG1), recombinase; This family is one of the two ...
386-1024 0e+00

Recombination-activation protein 1 (RAG1), recombinase; This family is one of the two different components of the RAG1-RAG2 V(D)J recombinase complex. The RAG complex, consisting of two RAG1 and two RAG2 proteins is a multi-protein complex that mediates DNA cleavage during V(D)J (variable-diversity-joining) recombination. RAG1 mediates DNA-binding to the conserved recombination signal sequences (RSS). Many of the proteins in this family are fragments. Solution of the structure of the complex of RAG1 and RAG2 shows that each protein dimerizes with itself and each pair then complexes together to from the RAG1-RAG2 V(D)J recombinase enzyme. The different structural elements in RAG1 for UniProtKB:P15919 are: an N-terminal nonamer-binding domain from residues 391-459; a dimerization and DNA-binding domain from 459-515; an extended pre-RNase H domain from 515-588; the catalytic RNase H domain from 588-719; a ZnC2 domain from 719-791; and ZnH2 domain from 791-962; and a three-helix C-terminal domain from 962-1008.


Pssm-ID: 315595  Cd Length: 653  Bit Score: 1155.18  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 341941803   386 INKGGRPRQHLLSLTRRAQKHRLRELKIQVKEFADKEEGGDVKAVCLTLFLLALRARNEHRQADELEAIMQGRGSGLQPA 465
Cdd:pfam12940    6 TNKGGRPRQHLLSLTRRAQKHRLRDLKHQVKVFADKEEGGDIKSVCLTLFLLALRAGNEHRQADELEAMMQGRGFGLHPA 85
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 341941803   466 VCLAIRVNTFLSCSQYHKMYRTVKAITGRQIFQPLHALRNAEKVLLPGYHPFEWQPPLKNVSSRTDVGIIDGLSGLASSV 545
Cdd:pfam12940   86 VCLAIRVNTFLSCSQYHKMYRTVKATSGRQIFQPLHTLRAAEKALLPGFHHFEWQPALKNVSPSCDVGIIDGLSGWSPSV 165
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 341941803   546 DEYPVDTIAKRFRYDSALVSALMDMEEDILEGMRSQDLDDY-LNGPFTVVVKESCDGMGDVSEKHGSGPAVPEKAVRFSF 624
Cdd:pfam12940  166 DDQPADTITRRFRYDVALVAALKDLEEDILEGLKEQGLDDSaCTEGFSVMIKECCDGMGDVSEKHGGGPAVPEKAVRFSF 245
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 341941803   625 TVMRITI---EHGSQNVKVFEEPKPNSELCCKPLCLMLADESDHETLTAILSPLIAEREAMKSSELTLEMGGIPRTFKFI 701
Cdd:pfam12940  246 TIMSVSIladDEEGEEVAIFHELKPNSELCCKPLCLMFADESDHETLTAILAPIMAEREAMKESRLILSIGGLLRSFRFH 325
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 341941803   702 FRGTGYDEKLVREVEGLEASGSVYICTLCDTTRLEASQNLVFHSITRSHAENLQRYEVWRSNPYHESVEELRDRVKGVSA 781
Cdd:pfam12940  326 FRGTGYDEKLVRDMEGLEASGSTYICTLCDSSRAEASKNKVLHAITRSHEENLERYEIWRTNPFSESADDLRDRVKGISA 405
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 341941803   782 KPFIETVPSIDALHCDIGNAAEFYKIFQLEIGEVYKHPNASKEERKRWQATLDKHLRKRMNLKPIMRMNGNFARKLMTQE 861
Cdd:pfam12940  406 KPFLETQACIDALHCDIGNATEFYKIFQDEIGEVHKKANPSKEERKRWQAALDKQLRKKMKLKPVMRMNGNFARKLMTQE 485
                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 341941803   862 TVDAVCELIPSEERHEALRELMDLYLKMKPVWRSSCPAKECPESLCQYSFNSQRFAELLSTKFKYRYEGKITNYFHKTLA 941
Cdd:pfam12940  486 AVDAVCELVPSEERQEALRELMHLYLQMKPVWRATCPAKECPDLLCRYSFNSQRFADLLSTTFKYRYDGKITNYLHKTLA 565
                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 341941803   942 HVPEIIERDGSIGAWASEGNESGNKLFRRFRKMNARQSKCYEMEDVLKHHWLYTSKYLQKFMNAH-NALKSSGFTMNSKE 1020
Cdd:pfam12940  566 HVPEIIERDGSIGAWASEGNESANKLFRRFRKMNARQSKSFELEDILKHHWLYTSKYLQKFMEAHkDSAKALEATIDPVE 645

                   ....
gi 341941803  1021 TLGD 1024
Cdd:pfam12940  646 IQDD 649
RAG1_imp_bd pfam12560
RAG1 importin binding; This region of RAG1 is responsible for binding to importin alpha.
12-287 1.70e-129

RAG1 importin binding; This region of RAG1 is responsible for binding to importin alpha.


Pssm-ID: 432636  Cd Length: 282  Bit Score: 393.70  E-value: 1.70e-129
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 341941803    12 SSAPDEIQHPQIKFSEWKFKLFRVRSFEKAPEEAQK-EKDSSEGKPYLEQSPVVP-EKPGGQNSILTQRALKLHPKFSKK 89
Cdd:pfam12560    1 SSMPDELQHPYKKFSEWKFKLFRVRSFEKAPLESETtEKGVALGLSSPEAPPTELgDGTAPGGSVLTLCGGKKKKEVVEK 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 341941803    90 FHADGKSSDKAVHQARLRHFCRICGNRFKSdGHSRRYPVHGPVDAKTQSLFRKKEKRVTSWPDLIARIFRIDVKADVDSI 169
Cdd:pfam12560   81 RRDDGKQQEKATHQALLRLLCRICGMSLKT-KKGRRHPVHGPVDDSTKCLLRKKEKKATSWPDLILKVFKVDVKGDVDSI 159
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 341941803   170 HPTEFCHDCWSIMHRkfssSHSQVYFPRKVTVEWHPHTPSCDICFTAHRGLKRKRHQPNVQLSKKLKTVLNHARRDRRKR 249
Cdd:pfam12560  160 HPTFFCHRCWTVIRR----GGGECSFPRTRVPEWKPHSSSCDLCPTKRRGLKRKGLPPNLQLAKRLKTDSDRARRGRRRK 235
                          250       260       270       280
                   ....*....|....*....|....*....|....*....|....*..
gi 341941803   250 ---------TQARVSSKEVLKKISNCSKIHLSTKLLAVDFPAHFVKS 287
Cdd:pfam12560  236 qwrsaitwwKQAAIQRKWVVKKITNCKKIHLSTKLLAVDYPVDFVKS 282
RING-HC_RAG1 cd16530
RING finger, HC subclass, found in recombination activating gene-1 (RAG-1) and similar ...
286-331 9.37e-27

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: 103.29  E-value: 9.37e-27
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 341941803  286 KSISCQICEHILADPVETSCKHLFCRICILRCLKVMGSYCPSCRYP 331
Cdd:cd16530     1 KSVSCQVCEHILADPVQTPCKHLFCRTCILKCLKVMGSYCPSCRYP 46
zf-RAG1 pfam10426
Recombination-activating protein 1 zinc-finger domain; This is a C2-H2 zinc-finger domain ...
351-380 7.03e-11

Recombination-activating protein 1 zinc-finger domain; This is a C2-H2 zinc-finger domain closely resembling the classical TFIIIA-type zinc-finger, CX3FX5LX2-3H, despite having a valine and a tyrosine at the core instead of a phenylalanine and a leucine, hence CX3VX1LX2YX2H. The structure, nevertheless, contains the characteristic two-stranded beta-sheet and alpha-helix of a classical zinc-finger. The domain binds one zinc and, in complex with the zinc-RING-finger domain, helps to stabilize the whole of the dimerization region of recombination activating protein 1 (RAG1). The function of the whole is to bind double-stranded DNA.


Pssm-ID: 431278  Cd Length: 30  Bit Score: 57.52  E-value: 7.03e-11
                           10        20        30
                   ....*....|....*....|....*....|
gi 341941803   351 LMVKCPAQDCNEEVSLEKYNHHVSSHKESK 380
Cdd:pfam10426    1 LVIRCPAKDCDEEVRLEKYGQHLSSHKEGK 30
RING-HC_RNF138 cd16544
RING finger, HC subclass, found in RING finger protein 138 (RNF138) and similar proteins; ...
290-331 3.29e-10

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: 56.26  E-value: 3.29e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 341941803  290 CQICEHILADPVETS-CKHLFCRICILRCLKVMGSYCPSCRYP 331
Cdd:cd16544     5 CPVCQEVLKDPVELPpCRHIFCKACILLALRSSGARCPLCRGP 47
zf-C3HC4 pfam00097
Zinc finger, C3HC4 type (RING finger); The C3HC4 type zinc-finger (RING finger) is a ...
290-328 2.05e-09

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: 53.90  E-value: 2.05e-09
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|
gi 341941803   290 CQICEHILADPVETS-CKHLFCRICILRCLKVMGSYCPSC 328
Cdd:pfam00097    1 CPICLEEPKDPVTLLpCGHLFCSKCIRSWLESGNVTCPLC 40
RING-HC_TRIM40-C-V cd16583
RING finger, HC subclass, found in tripartite motif-containing protein 40 (TRIM40) and similar ...
290-332 6.84e-09

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: 52.91  E-value: 6.84e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 341941803  290 CQICEHILADPVETSCKHLFCRICILRCLKVMGS----YCPSCRYPC 332
Cdd:cd16583     8 CPICQEPLKEAVSTDCGHLFCRMCLTQHAKKASAsgvfSCPVCRKPC 54
rad18 TIGR00599
DNA repair protein rad18; All proteins in this family for which functions are known are ...
287-364 7.57e-09

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: 58.86  E-value: 7.57e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 341941803   287 SISCQICEHILADPVETSCKHLFCRICILRCLKVMGSyCPSCRYPCFPTDL------ESPVKSFLNILNSLM----VKCP 356
Cdd:TIGR00599   26 SLRCHICKDFFDVPVLTSCSHTFCSLCIRRCLSNQPK-CPLCRAEDQESKLrsnwlvSEIVESFKNLRPSLLeflrIPKT 104

                   ....*...
gi 341941803   357 AQDCNEEV 364
Cdd:TIGR00599  105 TPVENPDL 112
RING-HC cd16449
HC subclass of RING (RING-HC) finger and its variants; The RING finger is a specialized type ...
289-328 1.17e-08

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: 51.72  E-value: 1.17e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 341941803  289 SCQICEHILADPVETSCKHLFCRICILRCLKVMGSYCPSC 328
Cdd:cd16449     2 ECPICLERLKDPVLLPCGHVFCRECIRRLLESGSIKCPIC 41
RING-HC_LONFs_rpt2 cd16514
second RING finger, HC subclass, found in the LON peptidase N-terminal domain and RING finger ...
290-331 1.30e-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: 51.50  E-value: 1.30e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 341941803  290 CQICEHILADPVETSCKHLFCRICILRCLKvMGSYCPSCRYP 331
Cdd:cd16514     4 CSLCLRLLYEPVTTPCGHTFCRACLERCLD-HSPKCPLCRTS 44
RING-HC_TRIM7-like_C-IV cd16594
RING finger, HC subclass, found in tripartite motif-containing proteins, TRIM7, TRIM11 and ...
288-332 1.92e-08

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: 51.53  E-value: 1.92e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 341941803  288 ISCQICEHILADPVETSCKHLFCRICILRCLKVMG--SYCPSCRYPC 332
Cdd:cd16594     6 LTCPICLDYFTDPVTLDCGHSFCRACIARCWEEPEtsASCPQCRETC 52
mRING-HC-C3HC3D_TRAF6 cd16643
Modified RING finger, HC subclass (C3HC3D-type), found in tumor necrosis factor (TNF) ...
290-326 7.02e-08

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: 50.07  E-value: 7.02e-08
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 341941803  290 CQICEHILADPVETSCKHLFCRICILRCLKVMGSYCP 326
Cdd:cd16643     4 CPICLMALREPVQTPCGHRFCKACILKSIREAGHKCP 40
RING-HC_PRT1-like cd23132
RING finger, HC subclass, found in Arabidopsis thaliana proteolysis 1 protein (PRT1) and ...
290-334 1.59e-07

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: 48.57  E-value: 1.59e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 341941803  290 CQICEHILADPVETSCKHLFCRICILRCLKVMG-SYCPSCR--YPCFP 334
Cdd:cd23132     5 CCICLDLLYKPVVLECGHVFCFWCVHRCMNGYDeSHCPLCRrpYDHFP 52
RING smart00184
Ring finger; E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and ...
290-328 1.85e-07

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: 48.27  E-value: 1.85e-07
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|
gi 341941803    290 CQIC-EHILADPVETSCKHLFCRICILRCLKVMGSYCPSC 328
Cdd:smart00184    1 CPIClEEYLKDPVILPCGHTFCRSCIRKWLESGNNTCPIC 40
RING-HC_HLTF cd16509
RING finger, HC subclass, found in helicase-like transcription factor (HLTF) and similar ...
290-337 2.97e-07

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: 48.07  E-value: 2.97e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 341941803  290 CQICEHILADPVETSCKHLFCRICILRCLKVMGSYCPSCRYPCFPTDL 337
Cdd:cd16509     6 CAICLDSLTNPVITPCAHVFCRRCICEVIQREKAKCPMCRAPLSASDL 53
RING-HC_BARD1 cd16496
RING finger, HC subclass, found in BRCA1-associated RING domain protein 1 (BARD-1) and similar ...
286-339 3.24e-07

RING finger, HC subclass, found in BRCA1-associated RING domain protein 1 (BARD-1) and similar proteins; BARD-1 is a critical factor in BRCA1-mediated tumor suppression and may also serve as a target for tumorigenic lesions in some human cancers. It associates with BRCA1 (breast cancer-1) to form a heterodimeric BRCA1/BARD1 complex that is responsible for maintaining genomic stability through nuclear functions involving DNA damage signaling and repair, transcriptional regulation, and cell cycle control. The BRCA1/BARD1 complex catalyzes autoubiquitination of BRCA1 and trans ubiquitination of other protein substrates. Its E3 ligase activity is dramatically reduced in the presence of UBX domain protein 1 (UBXN1). BARD-1 contains an C3HC4-type RING-HC finger that binds BRCA1 at its N-terminus and three tandem ankyrin repeats and tandem BRCT repeat domains at its C-terminus. The BRCT repeats bind CstF-50 (cleavage stimulation factor) to modulate mRNA processing and RNAP II stability in response to DNA damage.


Pssm-ID: 438159 [Multi-domain]  Cd Length: 86  Bit Score: 48.87  E-value: 3.24e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 341941803  286 KSISCQICEHILADPVET-SCKHLFCRICILRCLkvmGSYCPSCRYPCFPTDLES 339
Cdd:cd16496    14 NLLRCSRCASILKEPVTLgGCEHVFCRSCVGDRL---GNGCPVCDTPAWARDLQI 65
RING-HC_BRCA1 cd16498
RING finger, HC subclass, found in breast cancer type 1 susceptibility protein (BRCA1) and ...
286-331 3.50e-07

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: 49.22  E-value: 3.50e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 341941803  286 KSISCQICEHILADPVETSCKHLFCRICILRCL--KVMGSYCPSCRYP 331
Cdd:cd16498    15 KNLECPICLELLKEPVSTKCDHQFCRFCILKLLqkKKKPAPCPLCKKS 62
RING-HC_ScRAD18-like cd23148
RING finger, HC subclass, found in Saccharomyces cerevisiae radiation sensitivity protein 18 ...
286-337 4.12e-07

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: 47.53  E-value: 4.12e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 341941803  286 KSISCQICEHILADPVETSCKHLFCRICILRCLKVMGSyCPSCRYPCFPTDL 337
Cdd:cd23148     2 HALRCHICKDLLKAPMRTPCNHTFCSFCIRTHLNNDAR-CPLCKAEVTESGL 52
RING-HC_TRIM38_C-IV cd16600
RING finger, HC subclass, found in tripartite motif-containing protein 38 (TRIM38) and similar ...
289-332 5.19e-07

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: 47.46  E-value: 5.19e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 341941803  289 SCQICEHILADPVETSCKHLFCRICILRCLKVMGSY--------CPSCRYPC 332
Cdd:cd16600     7 TCSICLQLMTEPVSINCGHSYCKRCIVSFLENQSQLepgletfsCPQCRAPF 58
RING-HC_MmTRIM43-like cd23133
RING finger, HC subclass, found in Mus musculus tripartite motif-containing protein 43 (TRIM43) ...
286-332 6.40e-07

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: 47.21  E-value: 6.40e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 341941803  286 KSISCQICEHILADPVETSCKHLFCRICILRCLKVM--GSYCPSCRYPC 332
Cdd:cd23133     2 ETLTCSICQGIFMNPVYLRCGHKFCEACLLLFQEDIkfPAYCPMCRQPF 50
RING-HC_TRIM21_C-IV cd16596
RING finger, HC subclass, found in tripartite motif-containing protein TRIM21 and similar ...
288-351 1.02e-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: 47.20  E-value: 1.02e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 341941803  288 ISCQICEHILADPVETSCKHLFCRICILRCLKVMGSYCPSCRYPCFPTDLEsPVKSFLNILNSL 351
Cdd:cd16596    10 VTCPICLDPFVEPVSIECGHSFCQECISQVGKGGGSVCPVCRQRFLLKNLR-PNRQLANMVNNL 72
RING-HC_RNF125 cd16542
RING finger, HC subclass, found in RING finger protein 125 (RNF125); RNF125, also known as ...
287-329 1.04e-06

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: 46.41  E-value: 1.04e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 341941803  287 SISCQICEHILADPVETSCKHLFCRICILRCLKVMGSYCPSCR 329
Cdd:cd16542     1 NFDCAVCLEVLHQPVRTRCGHVFCRPCIATSLRNNTWTCPYCR 43
vRING-HC-C4C4_RBBP6 cd16620
Variant RING finger, HC subclass (C4C4-type), found in retinoblastoma-binding protein 6 (RBBP6) ...
289-337 1.19e-06

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: 46.24  E-value: 1.19e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 341941803  289 SCQICEHILADPVETSC-KHLFCRICILRCLKVMGSYCPSCRYPCFPTDL 337
Cdd:cd16620     5 KCPICKDLMKDAVLTPCcGNSFCDECIRTALLEEDFTCPTCKEPDVSPDA 54
RING-HC_RNF166 cd16549
RING finger, HC subclass, found in RING finger protein 166 (RNF166) and similar proteins; ...
289-331 1.97e-06

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: 45.57  E-value: 1.97e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 341941803  289 SCQICEHILADPVET-SCKHLFCRICILRCLKVMGSYCPSCRYP 331
Cdd:cd16549     3 SCPICLEVYHKPVVItSCGHTFCGECLQPCLQVASPLCPLCRMP 46
RING-HC_RNF39 cd16592
RING finger, HC subclass, found in RING finger protein 39 (RNF39) and similar proteins; RNF39, ...
290-332 2.67e-06

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: 45.52  E-value: 2.67e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 341941803  290 CQICEHILADPVETSCKHLFCRICILRCLKV--------MGSYCPSCRYPC 332
Cdd:cd16592     7 CPICLGYFKDPVILDCEHSFCRACIARHWGQeamegngaEGVFCPQCGEPC 57
RING-HC_RAD16-like cd16567
RING finger, HC subclass, found in Saccharomyces cerevisiae DNA repair protein RAD16, ...
288-331 2.78e-06

RING finger, HC subclass, found in Saccharomyces cerevisiae DNA repair protein RAD16, Schizosaccharomyces pombe rhp16, and similar proteins; Budding yeast RAD16, also known as ATP-dependent helicase RAD16, is encoded by a yeast excision repair gene homologous to the recombinational repair gene RAD54 and to the SNF2 gene involved in transcriptional activation. It is a component of the global genome repair (GGR) complex that promotes global genome nucleotide excision repair (GG-NER) by removing DNA damage from non-transcribing DNA. RAD16 is involved in differential repair of DNA after UV damage, and repairs preferentially the MAT-alpha locus compared with the HML-alpha locus. Fission yeast rhp16, also known as ATP-dependent helicase rhp16, is a RAD16 homolog. It is involved in GGR via nucleotide excision repair (NER), in conjunction with rhp7, after UV irradiation. Both RAD16 and rhp16 contain a C3HC4-type RING-HC finger, as well as a DEAD-like helicase domain and a helicase superfamily C-terminal domain.


Pssm-ID: 438229 [Multi-domain]  Cd Length: 48  Bit Score: 45.02  E-value: 2.78e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 341941803  288 ISCQICEHILADPVETSCKHLFCRICI---LRCLKVMGSYCPSCRYP 331
Cdd:cd16567     1 LVCGICHEEAEDPVVARCHHVFCRACVkeyIESAPGGKVTCPTCHKP 47
RING-HC_TRIM60-like_C-IV cd16607
RING finger, HC subclass, found in tripartite motif-containing proteins TRIM60, TRIM61, TRIM75 ...
288-332 2.84e-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: 45.11  E-value: 2.84e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 341941803  288 ISCQICEHILADPVETSCKHLFCRICI-LRCLKVMGSY-CPSCRYPC 332
Cdd:cd16607     2 ASCPICLDYLKDPVTINCGHNFCRSCIsMSWKDLQDTFpCPVCRFCC 48
RING-HC_TRIM4_C-IV cd16590
RING finger, HC subclass, found in tripartite motif-containing protein TRIM4 and similar ...
286-337 4.17e-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: 45.02  E-value: 4.17e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 341941803  286 KSISCQICEHILADPVETSCKHLFCRICILRCLKVMGS--YCPSCRYPCFPTDL 337
Cdd:cd16590     5 EELTCPICLDYFQDPVSIECGHNFCRGCLHRNWAPGGGpfPCPECRHPSAPAAL 58
RING-HC_AtBARD1-like cd23146
RING finger, HC subclass, found in Arabidopsis thaliana BRCA1-associated RING domain protein 1 ...
290-337 4.19e-06

RING finger, HC subclass, found in Arabidopsis thaliana BRCA1-associated RING domain protein 1 (AtBARD1) and similar proteins; AtBARD1, also called protein REPRESSOR OF WUSCHEL 1, binds specifically to H3K4me3 regions of target gene (e.g. WUS and WOX5) promoters to repress their transcription via chromatin remodeling. It is required for the shoot apical meristem (SAM) organization and maintenance, by confining WUS expression to the organizing center, and for the quiescent center (QC) development in the root apical meristem (RAM), by repressing WOX5 expression in the root proximal meristem. AtBARD1 plays a role in DNA repair and in cell-cycle control. It is required for the repair of DNA double-strand breaks (DSBs), both natural and induced by genotoxic stress, by homologous recombination (HR). AtBARD1 contains a typical C3HC4-type RING-HC finger.


Pssm-ID: 438508 [Multi-domain]  Cd Length: 54  Bit Score: 44.77  E-value: 4.19e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 341941803  290 CQICEHILADPVETSCKHLFCRICILRCLKVmGSYCPSCRYPCFPTDL 337
Cdd:cd23146     7 CPICLKLLNRPVLLPCDHIFCSSCITDSTKV-GSDCPVCKLPYHSQDL 53
RING-HC_RNF151 cd16547
RING finger, HC subclass, found in RING finger protein 151 (RNF151) and similar proteins; ...
290-331 5.58e-06

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: 44.37  E-value: 5.58e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 341941803  290 CQICEHILADPVETSCKHLFCRICILRCLKVMGSyCPSCRYP 331
Cdd:cd16547     6 CSICHGVLRCPVRLSCSHIFCKKCILQWLKRQET-CPCCRKE 46
RING-HC_TRIM69_C-IV cd16611
RING finger, HC subclass, found in tripartite motif-containing protein 69 (TRIM69) and similar ...
288-332 6.43e-06

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: 44.36  E-value: 6.43e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 341941803  288 ISCQICEHILADPVETSCKHLFCRICILRC--LKVMGSYCPSCRYPC 332
Cdd:cd16611     5 LHCPLCLDFFRDPVMLSCGHNFCQSCITGFweLQAEDTTCPECRELC 51
RING-HC_TRIM62_C-IV cd16608
RING finger, HC subclass, found in tripartite motif-containing protein 62 (TRIM62) and similar ...
286-332 7.18e-06

RING finger, HC subclass, found in tripartite motif-containing protein 62 (TRIM62) and similar proteins; TRIM62, also known as Ductal Epithelium Associated Ring Chromosome 1 (DEAR1), is a cytoplasmic E3 ubiquitin-protein ligase that was identified as a dominant regulator of acinar morphogenesis in the mammary gland. It is implicated in the inflammatory response of immune cells by regulating the Toll-like receptor 4 (TLR4) signaling pathway, leading to increased activity of the activator protein 1 (AP-1) transcription factor in primary macrophages. It is also involved in muscular protein homeostasis, especially during inflammation-induced atrophy, and may play a role in the pathogenesis of ICU-acquired weakness (ICUAW) by activating and maintaining inflammation in myocytes. Moreover, TRIM62 facilitates K27-linked poly-ubiquitination of CARD9 and also regulates CARD9-mediated anti-fungal immunity and intestinal inflammation. It also functions as a chromosome 1p35 tumor suppressor and negatively regulates transforming growth factor beta (TGFbeta)-driven epithelial-mesenchymal transition (EMT) by binding to and promoting the ubiquitination of SMAD3, a major effector of TGFbeta-mediated EMT. TRIM62 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: 438270 [Multi-domain]  Cd Length: 52  Bit Score: 44.03  E-value: 7.18e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 341941803  286 KSISCQICEHILADPVETSCKHLFCRICILRCLKVMGSY-CPSCRYPC 332
Cdd:cd16608     5 DELLCSICLSIYQDPVSLGCEHYFCRQCITEHWSRSEHRdCPECRRTF 52
RING-HC_RNF114 cd16540
RING finger, HC subclass, found in RING finger protein 114 (RNF114) and similar proteins; ...
290-331 8.10e-06

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: 43.60  E-value: 8.10e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 341941803  290 CQICEHILADPVETSCKHLFCRICILRCLKVMGSYCPSCRYP 331
Cdd:cd16540     4 CPVCLEIFETPVRVPCGHVFCNACLQECLKPKKPVCAVCRSP 45
RING-HC_RING1-like cd16531
RING finger, HC subclass, found in really interesting new gene proteins RING1, RING2 and ...
288-332 1.00e-05

RING finger, HC subclass, found in really interesting new gene proteins RING1, RING2 and similar proteins; RING1, also known as polycomb complex protein RING1, RING finger protein 1 (RNF1), or RING finger protein 1A (RING1A), is a transcriptional repressor that is associated with the Polycomb group (PcG) protein complex involved in stable repression of gene activity. 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. Both RING1 and RING2 are core components 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. RING2 acts as the main E3 ubiquitin ligase on histone H2A of the PRC1 complex, while RING1 may rather act as a modulator of RNF2/RING2 activity. Members of this family contain a C3HC4-type RING-HC finger.


Pssm-ID: 438193 [Multi-domain]  Cd Length: 66  Bit Score: 44.18  E-value: 1.00e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 341941803  288 ISCQICEHILADPVETS-CKHLFCRICILRCLKVMGSYCPSCRYPC 332
Cdd:cd16531     2 LMCPICLGIIKNTMTVKeCLHRFCAECIEKALRLGNKECPTCRKHL 47
RAD18 COG5432
RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms];
287-331 1.04e-05

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


Pssm-ID: 227719 [Multi-domain]  Cd Length: 391  Bit Score: 48.93  E-value: 1.04e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 341941803  287 SISCQICEHILADPVETSCKHLFCRICILRCLKVMgSYCPSCRYP 331
Cdd:COG5432    25 MLRCRICDCRISIPCETTCGHTFCSLCIRRHLGTQ-PFCPVCRED 68
RING-HC_RNF219 cd16562
RING finger, HC subclass, found in RING finger protein 219 (RNF219) and similar proteins; ...
288-331 1.05e-05

RING finger, HC subclass, found in RING finger protein 219 (RNF219) and similar proteins; RNF219 may function as a modulator of late-onset Alzheimer's disease (LOAD) associated amyloid beta A4 precursor protein (APP) endocytosis and metabolism. It genetically interacts with apolipoprotein E epsilon4 allele (APOE4). Thus, a genetic variant of RNF219 was found to affect amyloid deposition in human brain and LOAD age-of-onset. Moreover, common genetic variants at the RNF219 locus had been associated with alternations in lipid metabolism, cognitive performance and central nervous system ventricle volume. RNF219 contains a C3HC4-type RING-HC finger.


Pssm-ID: 438224 [Multi-domain]  Cd Length: 45  Bit Score: 43.58  E-value: 1.05e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 341941803  288 ISCQICEHILADPVETSCKHLFCRICILRCLKVmGSYCPSCRYP 331
Cdd:cd16562     2 ISCHICLGKVRQPVICSNNHVFCSSCMDVWLKN-NNQCPACRVP 44
RING-HC_TRIM41-like_C-IV cd16602
RING finger, HC subclass, found in tripartite motif-containing proteins TRIM41, TRIM52 and ...
290-329 1.19e-05

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: 43.38  E-value: 1.19e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 341941803  290 CQICEHILADPVETSCKHLFCRICIlrcLKVMGSYCPSCR 329
Cdd:cd16602     6 CAICLDYFKDPVSIGCGHNFCRVCV---TQLWGFTCPQCR 42
RING-HC_TRIM26_C-IV cd16598
RING finger, HC subclass, found in tripartite motif-containing protein 26 (TRIM26) and similar ...
288-331 1.20e-05

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: 44.00  E-value: 1.20e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 341941803  288 ISCQICEHILADPVETSCKHLFCRICILRCLKVMGSY----CPSCRYP 331
Cdd:cd16598     5 VTCSICLDYLRDPVTIDCGHNFCRSCITDYCPISGGHerpvCPLCRKP 52
RING-HC_TRIM8_C-V cd16580
RING finger, HC subclass, found in tripartite motif-containing protein 8 (TRIM8) and similar ...
284-331 1.30e-05

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: 43.73  E-value: 1.30e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 341941803  284 FVKSISCQICEHILADPVETSCKHLFCRICILRCL--KVMGSYCPSCRYP 331
Cdd:cd16580     8 FEEELICPICLHVFVEPVQLPCKHNFCRGCIGEAWakDAGLVRCPECNQA 57
RING-HC_TRIM65_C-IV cd16609
RING finger, HC subclass, found in tripartite motif-containing protein TRIM65 and similar ...
290-331 1.37e-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: 43.51  E-value: 1.37e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 341941803  290 CQICEHILADPVETSCKHLFCRICILRCLKV--MGSY-CPSCRYP 331
Cdd:cd16609     6 CSICLGLYQDPVTLPCQHSFCRACIEDHWRQkdEGSFsCPECRAP 50
RING-HC_TRIM77_C-IV cd16543
RING finger, HC subclass, found in tripartite motif-containing protein 77 (TRIM77) and similar ...
287-335 1.79e-05

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: 43.15  E-value: 1.79e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 341941803  287 SISCQICEHILADPVETSCKHLFCRICIlRCL---KVMGSYCPSCRYPcFPT 335
Cdd:cd16543     3 QLTCSICLDLLKDPVTIPCGHSFCMNCI-TLLwdrKQGVPSCPQCRES-FPP 52
RING-HC_TRIM72_C-IV cd16612
RING finger, HC subclass, found in tripartite motif-containing protein 72 (TRIM72) and similar ...
286-337 1.88e-05

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: 43.19  E-value: 1.88e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 341941803  286 KSISCQICEHILADPVETSCKHLFCRICILRCLK---VMGSYCPSCRYPCFPTDL 337
Cdd:cd16612     3 QDLSCPLCLKLFQSPVTTECGHTFCQDCLSRVPKeedGGSTSCPTCQAPTKPEQL 57
RING-HC_AtRMA-like cd16745
RING finger, HC subclass, found in Arabidopsis thaliana RING membrane-anchor proteins (AtRMAs) ...
289-328 1.91e-05

RING finger, HC subclass, found in Arabidopsis thaliana RING membrane-anchor proteins (AtRMAs) and similar proteins; AtRMAs, including AtRma1, AtRma2, and AtRma3, are endoplasmic reticulum (ER)-localized Arabidopsis homologs of human outer membrane of the ER-anchor E3 ubiquitin-protein ligase, RING finger protein 5 (RNF5). AtRMAs possess E3 ubiquitin ligase activity, and may play a role in the growth and development of Arabidopsis. The AtRMA1 and AtRMA3 genes are predominantly expressed in major tissues, such as cotyledons, leaves, shoot-root junction, roots, and anthers, while AtRMA2 expression is restricted to the root tips and leaf hydathodes. AtRma1 probably functions with the Ubc4/5 subfamily of E2. AtRma2 is likely involved in the cellular regulation of ABP1 expression levels through interacting with auxin binding protein 1 (ABP1). AtRMA proteins contain an N-terminal C3HC4-type RING-HC finger and a trans-membrane-anchoring domain in their extreme C-terminal region.


Pssm-ID: 438403 [Multi-domain]  Cd Length: 45  Bit Score: 42.86  E-value: 1.91e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 341941803  289 SCQICEHILADPVETSCKHLFCRICILRCLKVmGSYCPSC 328
Cdd:cd16745     2 ECNICLDLAQDPVVTLCGHLFCWPCLHKWLRR-QSSQPEC 40
RING-HC_RNF170 cd16553
RING finger, HC subclass, found in RING finger protein 170 (RNF170) and similar proteins; ...
287-333 2.09e-05

RING finger, HC subclass, found in RING finger protein 170 (RNF170) and similar proteins; RNF170, also known as putative LAG1-interacting protein, is an endoplasmic reticulum (ER) membrane-bound E3 ubiquitin-protein ligase that mediates ubiquitination-dependent degradation of type-I inositol 1,4,5-trisphosphate (IP3) receptors (ITPR1) via the endoplasmic-reticulum-associated protein degradation (ERAD) pathway. A point mutation (arginine to cysteine at position 199) in the RNF170 gene is linked with autosomal-dominant sensory ataxia (ADSA), a disease characterized by neurodegeneration in the posterior columns of the spinal cord. RNF170 contains a C3HC4-type RING-HC finger.


Pssm-ID: 438215 [Multi-domain]  Cd Length: 57  Bit Score: 43.05  E-value: 2.09e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 341941803  287 SISCQICEHILADPVETSCKHLFCRICIL---RCLKVMGSY-CPSCR------YPCF 333
Cdd:cd16553     1 DMECPICLQDARFPVETNCGHLFCGPCIItywRHGSWLGAVsCPVCRqtvtllLPVF 57
RING-HC_AtBRCA1-like cd23147
RING finger, HC subclass, found in Arabidopsis thaliana protein BREAST CANCER SUSCEPTIBILITY 1 ...
286-331 2.25e-05

RING finger, HC subclass, found in Arabidopsis thaliana protein BREAST CANCER SUSCEPTIBILITY 1 homolog (AtBRCA1) and similar proteins; AtBRCA1 plays a role in DNA repair and in cell-cycle control. It is required for the repair of DNA double-strand breaks (DSBs), both natural and induced by genotoxic stress, by homologous recombination (HR). AtBRCA1 contains a typical C3HC4-type RING-HC finger.


Pssm-ID: 438509 [Multi-domain]  Cd Length: 54  Bit Score: 42.84  E-value: 2.25e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 341941803  286 KSISCQICEHILADPVETSCKHLFCRICILRCLKVMgSYCPSCRYP 331
Cdd:cd23147     3 KELKCPICLSLFKSAANLSCNHCFCAGCIGESLKLS-AICPVCKIP 47
mRING-HC-C3HC3D_TRAF7 cd16644
Modified RING finger, HC subclass (C3HC3D-type), found in tumor necrosis factor (TNF) ...
290-327 2.28e-05

Modified RING finger, HC subclass (C3HC3D-type), found in tumor necrosis factor (TNF) receptor-associated factor 7 (TRAF7) and similar proteins; TRAF7, also known as RING finger and WD repeat-containing protein 1 or RING finger protein 119 (RNF119), is an E3 ubiquitin-protein ligase involved in signal transduction pathways that lead either to activation or repression of NF-kappaB transcription factor by promoting K29-linked ubiquitination of several cellular targets, including the NF-kappaB essential modulator (NEMO) and the p65 subunit of NF-kappaB transcription factor. It is also involved in K29-linked polyubiquitination that has been implicated in lysosomal degradation of proteins. Moreover, TRAF7 is required for K48-linked ubiquitination of p53, a key tumor suppressor and a master regulator of various signaling pathways, such as those related to apoptosis, cell cycle and DNA repair. It is also required for tumor necrosis factor alpha (TNFalpha)-induced Jun N-terminal kinase activation and promotes cell death by regulating polyubiquitination and lysosomal degradation of c-FLIP protein. Furthermore, TRAF7 functions as small ubiquitin-like modifier (SUMO) E3 ligase involved in other post-translational modification, such as sumoylation. It binds to and stimulates sumoylation of the proto-oncogene product c-Myb, a transcription factor regulating proliferation and differentiation of hematopoietic cells. It potentiates MEKK3-induced AP1 and CHOP activation and induces apoptosis. Meanwhile, TRAF7 mediates MyoD1 regulation of the pathway and cell-cycle progression in myoblasts. It also plays a role in Toll-like receptors (TLR) signaling. TRAF7 contains an N-terminal domain with a modified C3HC3D-type RING-HC finger and an adjacent zinc finger, and a unique C-terminal domain that comprises a coiled coil domain and seven WD40 repeats.


Pssm-ID: 438306 [Multi-domain]  Cd Length: 47  Bit Score: 42.34  E-value: 2.28e-05
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 341941803  290 CQICEHILADPVETSCKHLFCRICILRclkVMGSYCPS 327
Cdd:cd16644     8 CPLCQRVFKDPVITSCGHTFCRRCALT---APGEKCPV 42
RING-HC_TRIM47-like_C-IV cd16604
RING finger, HC subclass, found in tripartite motif-containing protein 47 (TRIM47) and similar ...
288-331 2.40e-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: 42.41  E-value: 2.40e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 341941803  288 ISCQICEHILADPVETSCKHLFCRICI--LRCLKVMGSY-CPSCRYP 331
Cdd:cd16604     1 LSCPICLDLLKDPVTLPCGHSFCMGCLgaLWGAGRGGRAsCPLCRQT 47
RING-HC_RNF168 cd16550
RING finger, HC subclass, found in RING finger protein 168 (RNF168) and similar proteins; ...
290-329 2.47e-05

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: 42.36  E-value: 2.47e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 341941803  290 CQICEHILADPVETSCKHLFCRICILRCLKVMGSYCPSCR 329
Cdd:cd16550     3 CPICLEILVEPVTLPCNHTLCMPCFQSTVEKASLCCPLCR 42
zf-C3HC4_2 pfam13923
Zinc finger, C3HC4 type (RING finger);
290-328 2.66e-05

Zinc finger, C3HC4 type (RING finger);


Pssm-ID: 404756 [Multi-domain]  Cd Length: 40  Bit Score: 42.04  E-value: 2.66e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|
gi 341941803   290 CQICEHILADPVETS-CKHLFCRICILRCLKvMGSYCPSC 328
Cdd:pfam13923    2 CPICMDMLKDPSTTTpCGHVFCQDCILRALR-AGNECPLC 40
RING-HC_ScPSH1-like cd16568
RING finger, HC subclass, found in Saccharomyces cerevisiae POB3/SPT16 histone-associated ...
290-329 2.69e-05

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: 42.36  E-value: 2.69e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 341941803  290 CQICEHILADPVETSCKHLFCRICILRCLK-VMGSYCPSCR 329
Cdd:cd16568     7 CIICHEYLYEPMVTTCGHTYCYTCLNTWFKsNRSLSCPDCR 47
mRING-HC-C4C4_TRIM37_C-VIII cd16619
Modified RING finger, HC subclass (C4C4-type), found in tripartite motif-containing protein 37 ...
290-329 3.42e-05

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: 41.96  E-value: 3.42e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 341941803  290 CQICEHILADPVE-TSCKHLFCRICILRCLKVMGSYCPSCR 329
Cdd:cd16619     3 CFICMEKLRDPRLcPHCSKLFCKGCIRRWLSEQRSSCPHCR 43
mRING-HC-C3HC3D_LNX1-like cd16637
Modified RING finger, HC subclass (C3HC3D-type), found in ligand of Numb protein LNX1, LNX2, ...
290-326 4.63e-05

Modified RING finger, HC subclass (C3HC3D-type), found in ligand of Numb protein LNX1, LNX2, and similar proteins; The ligand of Numb protein X (LNX) family, also known as PDZ and RING (PDZRN) family, includes LNX1-5, which can interact with Numb, a key regulator of neurogenesis and neuronal differentiation. LNX5 (also known as PDZK4 or PDZRN4L) shows high sequence homology to LNX3 and LNX4, but it lacks the RING domain. LNX1-4 proteins function as E3 ubiquitin ligases and have a unique domain architecture consisting of an N-terminal RING-HC finger for E3 ubiquitin ligase activity and either two or four PDZ domains necessary for substrate-binding. LNX1/LNX2-like proteins contain a modified C3HC3D-type RING-HC finger and four PDZ domains. This model corresponds to the RING finger.


Pssm-ID: 438299 [Multi-domain]  Cd Length: 42  Bit Score: 41.61  E-value: 4.63e-05
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 341941803  290 CQICEHILADPVETSCKHLFCRICILRCLKVMgSYCP 326
Cdd:cd16637     4 CHICLQPLVEPLDTPCGHTFCYKCLTNYLKIQ-QCCP 39
RING-HC_RNF169 cd16551
RING finger, HC subclass, found in RING finger protein 169 (RNF169) and similar proteins; ...
287-331 5.16e-05

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: 41.76  E-value: 5.16e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 341941803  287 SISCQICEHILADPVETSCKHLFCRICILRCLKVMGSY--CPSCRYP 331
Cdd:cd16551     1 ELTCAGCLEVPVEPATLPCGHTLCRGCANRALDAAEAGptCPRCRAP 47
RING-HC_UHRF cd16613
RING finger, HC subclass, found in ubiquitin-like PHD and RING finger domain-containing ...
290-330 5.67e-05

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: 41.18  E-value: 5.67e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 341941803  290 CQICEHILADPVETSCKHLFCRICILRCLKVMGSYCPSCRY 330
Cdd:cd16613     3 CICCQELVYKPITTPCKHNICKSCLQRSFKAEVYTCPACRH 43
RING-HC_TRIM10_C-IV cd16593
RING finger, HC subclass, found in tripartite motif-containing protein 10 (TRIM10) and similar ...
290-334 6.63e-05

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: 41.82  E-value: 6.63e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 341941803  290 CQICEHILADPVETSCKHLFCRICILRCLKVMGS------YCPSCRYPCFP 334
Cdd:cd16593     8 CPICQGTLREPVTIDCGHNFCRACLTRYCEIPGPdleeppTCPLCKEPFRP 58
RING-HC_LNX3 cd16718
RING finger, HC subclass, found in ligand of numb protein X 3 (LNX3); LNX3, also known as PDZ ...
288-329 6.81e-05

RING finger, HC subclass, found in ligand of numb protein X 3 (LNX3); LNX3, also known as PDZ domain-containing RING finger protein 3 (PDZRN3), or Semaphorin cytoplasmic domain-associated protein 3 (SEMACAP3), is an E3 ubiquitin-protein ligase that was first identified as a Semaphorin-binding partner. It is also responsible for the ubiquitination and degradation of Numb, a component of the Notch signaling pathway that functions in the specification of cell fates during development and is known to control cell numbers during neurogenesis in vertebrates. LNX3 acts as a negative regulator of osteoblast differentiation by inhibiting Wnt-beta-catenin signaling. LNX3 also plays an important role in neuromuscular junction formation. It interacts with and ubiquitinates the muscle specific tyrosine kinase (MuSK), thus promoting its endocytosis and negatively regulating the cell surface expression of this key regulator of postsynaptic assembly. LNX3 contains an N-terminal C3HC4-type RING-HC finger, two PDZ domains, and a C-terminal LNX3 homology (LNX3H) domain.


Pssm-ID: 438378 [Multi-domain]  Cd Length: 47  Bit Score: 41.12  E-value: 6.81e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 341941803  288 ISCQICEHILADPVETSCKHLFCRICILRCLKVMGSyCPS-CR 329
Cdd:cd16718     5 FKCNLCNKVLEDPLTTPCGHVFCAGCVLPWVVQQGS-CPVkCQ 46
RING-HC_TRIM59_C-V cd16763
RING finger, HC subclass, found in tripartite motif-containing protein 59 (TRIM59) and similar ...
288-329 7.02e-05

RING finger, HC subclass, found in tripartite motif-containing protein 59 (TRIM59) and similar proteins; 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. It is upregulated in gastric cancer and promotes gastric carcinogenesis by interacting with and targeting the P53 tumor suppressor for its ubiquitination and degradation. It also acts as a novel accessory molecule involved in cytotoxicity of BCG-activated macrophages (BAM). Moreover, TRIM59 may serve as a multifunctional regulator for innate immune signaling pathways. It interacts with ECSIT and negatively regulates nuclear factor-kappaB (NF- kappa B) and interferon regulatory factor (IRF)-3/7-mediated signal pathways. TRIM59 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, TRIM59 contains a C-terminal transmembrane domain.


Pssm-ID: 438419 [Multi-domain]  Cd Length: 56  Bit Score: 41.44  E-value: 7.02e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 341941803  288 ISCQICEHILADPVETSCKHLFCRICILRCLKVMGSY-----------CPSCR 329
Cdd:cd16763     4 LTCSVCYSLFEDPRVLPCSHTFCRNCLENILQVSGNFsiwrplrpplkCPNCR 56
RING-HC_COP1 cd16504
RING finger, HC subclass, found in constitutive photomorphogenesis protein 1 (COP1) and ...
288-331 8.27e-05

RING finger, HC subclass, found in constitutive photomorphogenesis protein 1 (COP1) and similar proteins; COP1, also known as RING finger and WD repeat domain protein 2 (RFWD2) or RING finger protein 200 (RNF200), is a central regulator of photomorphogenic development in plants, which targets key transcription factors for proteasome-dependent degradation. It is localized predominantly in the nucleus, but may also be present in the cytosol. Mammalian COP1 functions as an E3 ubiquitin-protein ligase that interacts with Jun transcription factors and modulates their transcriptional activity. It also interacts with and negatively regulates the tumor-suppressor protein p53. Moreover, COP1 associates with COP9 signalosome subunit 6 (CSN6), and is involved in 14-3-3sigma ubiquitin-mediated degradation. The CSN6-COP1 link enhances ubiquitin-mediated degradation of p27(Kip1), a critical CDK inhibitor involved in cell cycle regulation, to promote cancer cell growth. Furthermore, COP1 functions as the negative regulator of ETV1 and influences prognosis in triple-negative breast cancer. COP1 contains an N-terminal extension, a C3HC4-type RING-HC finger, a coiled coil domain, and seven WD40 repeats. In human COP1, a classic leucine-rich NES, and a novel bipartite NLS is bridged by the RING-HC finger.


Pssm-ID: 438167 [Multi-domain]  Cd Length: 47  Bit Score: 41.07  E-value: 8.27e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 341941803  288 ISCQICEHILADPVETSCKHLFCRICILRCLKVmGSYCPSCRYP 331
Cdd:cd16504     3 FLCPICFDIIKEAFVTKCGHSFCYKCIVKHLEQ-KNRCPKCNFY 45
RING-HC_TRIM39_C-IV cd16601
RING finger, HC subclass, found in tripartite motif-containing protein 39 (TRIM39) and similar ...
289-328 1.20e-04

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: 40.55  E-value: 1.20e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 341941803  289 SCQICEHILADPVETSCKHLFCRICILRCL-KVMGSY-CPSC 328
Cdd:cd16601     3 SCSLCKEYLKDPVIIECGHNFCRACITRFWeELDGDFpCPQC 44
RING-HC_TRIM25_C-IV cd16597
RING finger, HC subclass, found in tripartite motif-containing protein TRIM25 and similar ...
289-338 1.27e-04

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: 41.14  E-value: 1.27e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 341941803  289 SCQICEHILADPVETSCKHLFCRICILRCLKVMGS---YCPSCRyPCFPTDLE 338
Cdd:cd16597     7 TCSICLELFKDPVTLPCGHNFCGVCIEKTWDSQHGseySCPQCR-ATFPRRPE 58
RING-HC_RAD18 cd16529
RING finger, HC subclass, found in postreplication repair protein RAD18 and similar proteins; ...
290-337 1.27e-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: 40.75  E-value: 1.27e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 341941803  290 CQIC-EHILADPVETSCKHLFCRICILRCLKvMGSYCPSCRYPCFPTDL 337
Cdd:cd16529     7 CPICfEYFNTAMMITQCSHNYCSLCIRRFLS-YKTQCPTCRAAVTESDL 54
RING-HC_TRIM43-like_C-IV cd16603
RING finger, HC subclass, found in tripartite motif-containing proteins TRIM43, TRIM48, TRIM49, ...
284-331 1.50e-04

RING finger, HC subclass, found in tripartite motif-containing proteins TRIM43, TRIM48, TRIM49, TRIM51, TRIM64 and similar proteins; The family includes a group of closely related uncharacterized tripartite motif-containing proteins, TRIM43, TRIM43B, TRIM48/RNF101, TRIM49/RNF18, TRIM49B, TRIM49C/TRIM49L2, TRIM49D/TRIM49L, TRIM51/SPRYD5, TRIM64, TRIM64B, and TRIM64C, whose biological function remain unclear. TRIM49, also known as testis-specific RING-finger protein, has moderate similarity with SS-A/Ro52 antigen, suggesting it may be one of the target proteins of autoantibodies in the sera of patients with these autoimmune disorders. All family members 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 as well as a SPRY/B30.2 domain positioned C-terminal to the RBCC domain. In RBCC region, they all have a C3HC4-type RING-HC finger.


Pssm-ID: 438265 [Multi-domain]  Cd Length: 59  Bit Score: 40.54  E-value: 1.50e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 341941803  284 FVKSISCQICEHILADPVETSCKHLFCRICILRCLKVMGS--YCPSCRYP 331
Cdd:cd16603     1 FQRELTCPICMNYFIDPVTIDCGHSFCRPCLYLNWQDIPFlaQCPECRKT 50
RING-HC_TRAF3 cd16640
RING finger, HC subclass, found in tumor necrosis factor (TNF) receptor-associated factor 3 ...
290-328 1.75e-04

RING finger, HC subclass, found in tumor necrosis factor (TNF) receptor-associated factor 3 (TRAF3) and similar proteins; TRAF3, also known as CAP-1, CD40 receptor-associated factor 1 (CRAF1), CD40-binding protein (CD40BP), or LMP1-associated protein 1 (LAP1), is a member of the TRAF protein family, which mainly functions in the immune system, where it mediates signaling through tumor necrosis factor receptors (TNFRs) and interleukin-1/Toll-like receptors (IL-1/TLRs). It also plays a unique cell type-specific and critical role in the restraint of B-cell homeostatic survival, a role with important implications for both B-cell differentiation and the pathogenesis of B-cell malignancies. TRAF3 differentially regulates differentiation of specific T cell subsets. It is required for iNKT cell development, restrains Treg cell development in the thymus, and plays an essential role in the homeostasis of central memory CD8+ T cells. TRAF3 contains an N-terminal domain with a typical C3HC4-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: 438302 [Multi-domain]  Cd Length: 42  Bit Score: 39.88  E-value: 1.75e-04
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 341941803  290 CQICEHILADPVETSCKHLFCRICILRCLKVMGSYCPSC 328
Cdd:cd16640     3 CEKCRLVLCNPKQTECGHRFCESCMNALLSSSNPQCPAC 41
RING-HC_TRIM13_like_C-V cd16581
RING finger, HC subclass, found in tripartite motif-containing proteins TRIM13, TRIM59 and ...
288-329 2.29e-04

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: 39.80  E-value: 2.29e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 341941803  288 ISCQICEHILADPVETSCKHLFCRICILRCLKVMGSY------CPSCR 329
Cdd:cd16581     3 LTCSICYNIFDDPKILPCSHTFCKNCLEKLLAASGYYllaslkCPTCR 50
RING-HC_TRIM58_C-IV cd16606
RING finger, HC subclass, found in tripartite motif-containing protein TRIM58 and similar ...
290-331 2.54e-04

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: 39.84  E-value: 2.54e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 341941803  290 CQICEHILADPVETSCKHLFCRICILR-CLKVMGSY-----CPSCRYP 331
Cdd:cd16606     5 CPVCLDFLQEPVSVDCGHSFCLRCISEfCEKSDSAQggvyaCPQCRGP 52
PEX10 COG5574
RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, ...
290-336 2.55e-04

RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 227861 [Multi-domain]  Cd Length: 271  Bit Score: 44.11  E-value: 2.55e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 341941803  290 CQICEHILADPVETSCKHLFCRICIL--RCLKVMGsYCPSCRYPCFPTD 336
Cdd:COG5574   218 CFLCLEEPEVPSCTPCGHLFCLSCLLisWTKKKYE-FCPLCRAKVYPKK 265
RING-HC_UHRF1 cd16769
RING finger, HC subclass, found in ubiquitin-like PHD and RING finger domain-containing ...
290-330 2.72e-04

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: 40.80  E-value: 2.72e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 341941803  290 CQICEHILADPVETSCKHLFCRICILRCLKVMGSYCPSCRY 330
Cdd:cd16769    15 CICCQELVFRPITTVCQHNVCKDCLDRSFRAQVFSCPACRY 55
RING-HC_UHRF2 cd16770
RING finger, HC subclass, found in ubiquitin-like PHD and RING finger domain-containing ...
286-330 2.79e-04

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: 40.18  E-value: 2.79e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 341941803  286 KSISCQICEHILADPVETSCKHLFCRICILRCLKVMGSYCPSCRY 330
Cdd:cd16770     2 ESFLCICCQELVYQPVTTECQHNVCKSCLQRSFKAEVYTCPACRH 46
RING-HC_TRIM68_C-IV cd16610
RING finger, HC subclass, found in tripartite motif-containing protein 68 (TRIM68) and similar ...
288-329 3.86e-04

RING finger, HC subclass, found in tripartite motif-containing protein 68 (TRIM68) and similar proteins; TRIM68, also known as RING finger protein 137 (RNF137) or SSA protein SS-56 (SS-56), is an E3 ubiquitin-protein ligase that negatively regulates Toll-like receptor (TLR)- and RIG-I-like receptor (RLR)-driven type I interferon production by degrading TRK fused gene (TFG), a novel driver of IFN-beta downstream of anti-viral detection systems. It also functions as a cofactor for androgen receptor-mediated transcription by regulating ligand-dependent transcription of androgen receptor in prostate cancer cells. Moreover, TRIM68 is a cellular target of autoantibody responses in Sjogre's syndrome (SS), as well as systemic lupus erythematosus (SLE). It is also an auto-antigen for T cells in SS and SLE. TRIM68 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: 438272 [Multi-domain]  Cd Length: 49  Bit Score: 39.11  E-value: 3.86e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 341941803  288 ISCQICEHILADPVETSCKHLFCRICILRCLKVMGSY------CPSCR 329
Cdd:cd16610     2 VACPICMTFLREPVSIDCGHSFCHSCLSGLWEVPGESqnwgytCPLCR 49
RING-HC_TRIM5-like_C-IV cd16591
RING finger, HC subclass, found in tripartite motif-containing proteins TRIM5, TRIM6, TRIM22, ...
286-347 3.92e-04

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: 39.73  E-value: 3.92e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 341941803  286 KSISCQICEHILADPVETSCKHLFCRICI-LRCLKVM----GSYCPSCRYPCFPTDLEsPVKSFLNI 347
Cdd:cd16591     5 EEVTCPICLELLTEPLSLDCGHSFCQACItANHKESVnqegESSCPVCRTSYQPENLR-PNRHLANI 70
RING-HC_TRIM17_C-IV cd16595
RING finger, HC subclass, found in tripartite motif-containing protein TRIM17 and similar ...
289-329 5.01e-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: 39.59  E-value: 5.01e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 341941803  289 SCQICEHILADPVETSCKHLFCRICILRC----------LKVMGSY-CPSCR 329
Cdd:cd16595     7 TCSICLDYFTDPVMTTCGHNFCRACIQLSwekargkkgrRKQKGSFpCPECR 58
RING-HC_PCGF5 cd16737
RING finger found in polycomb group RING finger protein 5 (PCGF5) and similar proteins; PCGF5, ...
288-328 5.68e-04

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: 40.13  E-value: 5.68e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 341941803  288 ISCQICEHILADP-VETSCKHLFCRICILRCLKvMGSYCPSC 328
Cdd:cd16737    11 ITCRICKGYLIKPtTVTECLHTFCKSCIVQHFE-DSNDCPEC 51
RING-HC_RNF5-like cd16534
RING finger, HC subclass, found in RING finger protein RNF5, RNF185 and similar proteins; RNF5 ...
289-329 6.82e-04

RING finger, HC subclass, found in RING finger protein RNF5, RNF185 and similar proteins; RNF5 and RNF185 are E3 ubiquitin-protein ligases that are anchored to the outer membrane of the endoplasmic reticulum (ER). RNF5 acts at early stages of cystic fibrosis (CF) transmembrane conductance regulator (CFTR) biosynthesis, and functions as a target for therapeutic modalities to antagonize mutant CFTR proteins in CF patients carrying the F508del allele. RNF185 controls the degradation of CFTR and CFTR F508del allele in a RING- and proteasome-dependent manner, but does not control that of other classical endoplasmic reticulum-associated degradation (ERAD) model substrates. Moreover, both RNF5 and RNF185 play important roles in cell adhesion and migration through the modulation of cell migration by ubiquitinating paxillin. Arabidopsis thaliana RING membrane-anchor proteins (AtRMAs) are also included in this family. They possess E3 ubiquitin-protein ligase activity and may play a role in the growth and development of Arabidopsis. All members of this family contain a C3HC4-type RING-HC finger.


Pssm-ID: 438196 [Multi-domain]  Cd Length: 44  Bit Score: 38.05  E-value: 6.82e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 341941803  289 SCQICEHILADPVETSCKHLFCRICILRCL--KVMGSYCPSCR 329
Cdd:cd16534     2 ECNICLDTASDPVVTMCGHLFCWPCLYQWLetRPDRQTCPVCK 44
RING-HC_RNF220 cd16563
RING finger, HC subclass, found in RING finger protein 220 (RNF220) and similar proteins; ...
289-337 7.61e-04

RING finger, HC subclass, found in RING finger protein 220 (RNF220) and similar proteins; RNF220 is an E3 ubiquitin-protein ligase that promotes the ubiquitination and proteasomal degradation of Sin3B, a scaffold protein of the Sin3/HDAC (histone deacetylase) corepressor complex. It can also bind E2 and mediate auto-ubiquitination of itself. Moreover, RNF220 specifically interacts with beta-catenin, and enhances canonical Wnt signaling through ubiquitin-specific protease 7 (USP7)-mediated deubiquitination and stabilization of beta-catenin, which is independent of its E3 ligase activity. RNF220 contains a characteristic C3HC4-type RING-HC finger at its C-terminus.


Pssm-ID: 438225 [Multi-domain]  Cd Length: 52  Bit Score: 38.20  E-value: 7.61e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 341941803  289 SCQICEHILADP-VETSCKHLFCRICILRCLKVMgSYCPSCRYPCFPTDL 337
Cdd:cd16563     2 KCLICMDSYTMPlVSIQCWHVHCEECWLRTLGAK-KLCPQCNTITSPADL 50
RING-HC_PCGF cd16525
RING finger, HC subclass, found in Polycomb Group RING finger homologs (PCGF1, 2, 3, 4, 5 and ...
288-329 8.11e-04

RING finger, HC subclass, found in Polycomb Group RING finger homologs (PCGF1, 2, 3, 4, 5 and 6), and similar proteins; This subfamily includes six Polycomb Group (PcG) RING finger homologs (PCGF1/NSPc1, PCGF2/Mel-18, PCGF3, PCGF4/BMI1, PCGF5, and PCGF6/MBLR) that use epigenetic mechanisms to maintain or repress expression of their target genes. They were first discovered in fruit flies and are well known for silencing Hox genes through modulation of chromatin structure during embryonic development. PCGF homologs play important roles in cell proliferation, differentiation, and tumorigenesis. They all have been found to associate with ring finger protein 2 (RNF2). The RNF2-PCGF heterodimer is catalytically competent as an E3 ubiquitin transferase and is the scaffold for the assembly of additional components. Moreover, PCGF homologs are critical components in the assembly of distinct Polycomb Repression Complex 1 (PRC1) related complexes which is involved in the maintenance of gene repression and which target different genes through distinct mechanisms. The Drosophila PRC1 core complex is formed by the Polycomb (Pc), Polyhomeotic (Ph), Posterior sex combs (Psc), and Sex combs extra (Sce, also known as Ring) subunits. In mammals, the composition of PRC1 is much more diverse and varies depending on the cellular context. All PRC1 complexes contain homologs of the Drosophila Ring protein. Ring1A/RNF1 and Ring1B/RNF2 are E3 ubiquitin ligases that mark lysine 119 of histone H2A with a single ubiquitin group (H2AK119ub). Mammalian homologs of the Drosophila Psc protein, such as PCGF2/Mel-18 or PCGF4/BMI1, regulate PRC1 enzymatic activity. PRC1 complexes can be divided into at least two classes according to the presence or absence of CBX proteins, which are homologs of Drosophila Pc. Canonical PRC1 complexes contain CBX proteins that recognize and bind H3K27me3, the mark deposited by PRC2. Therefore, canonical PRC1 complexes and PRC2 can act together to repress gene transcription and maintain this repression through cell division. Non-canonical PRC1 complexes, containing RYBP (together with additional proteins, such as L3mbtl2 or Kdm2b) rather than the CBX proteins have recently been described in mammals. PCGF homologs contain a C3HC4-type RING-HC finger.


Pssm-ID: 438188 [Multi-domain]  Cd Length: 42  Bit Score: 37.97  E-value: 8.11e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 341941803  288 ISCQICEHILADPVE-TSCKHLFCRICILRCLKVMgSYCPSCR 329
Cdd:cd16525     1 LTCSLCKGYLIDATTiTECLHSFCKSCIVRHLETS-KNCPVCD 42
RING-HC_TRIM35_C-IV cd16599
RING finger, HC subclass, found in tripartite motif-containing protein 35 (TRIM35) and similar ...
290-340 8.13e-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: 38.60  E-value: 8.13e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 341941803  290 CQICEHILADPVETSCKHLFCRICILRCLKVMGSY-CPSCRYPCFPTDLESP 340
Cdd:cd16599     7 CPICYEPFREAVTLRCGHNFCKGCVSRSWERQPRApCPVCKEASSSDDLRTN 58
RING-HC_CHFR cd16503
RING finger, HC subclass, found in checkpoint with forkhead and RING finger domains protein ...
290-332 8.81e-04

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: 38.12  E-value: 8.81e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 341941803  290 CQICEHILADPVETS-CKHLFCRICILRCLKVMGSYCPSCRYPC 332
Cdd:cd16503     5 CSICQDLLHDCVSLQpCMHNFCAACYSDWMERSNTECPTCRATV 48
zf-RING_UBOX pfam13445
RING-type zinc-finger; This zinc-finger is a typical RING-type of plant ubiquitin ligases.
290-326 9.35e-04

RING-type zinc-finger; This zinc-finger is a typical RING-type of plant ubiquitin ligases.


Pssm-ID: 433213 [Multi-domain]  Cd Length: 38  Bit Score: 37.76  E-value: 9.35e-04
                           10        20        30
                   ....*....|....*....|....*....|....*....
gi 341941803   290 CQICEHILADPVeTSCKHLFCRICILRCLKVMGSY--CP 326
Cdd:pfam13445    1 CPICLELFTDPV-LPCGHTFCRECLEEMSLLKGGRfkCP 38
zf-RING_6 pfam14835
zf-RING of BARD1-type protein; The RING domain of the breast and ovarian cancer ...
282-338 1.10e-03

zf-RING of BARD1-type protein; The RING domain of the breast and ovarian cancer tumor-suppressor BRCA1 interacts with multiple cognate proteins, including the RING protein BARD1. Proper function of the BRCA1 RING domain is critical, as evidenced by the many cancer-predisposing mutations found within this domain. A dimer is formed between the RING domains of BRCA1 and BARD1. The BRCA1-BARD1 structure provides a model for its ubiquitin ligase activity, illustrates how the BRCA1 RING domain can be involved in associations with multiple protein partners and provides a framework for understanding cancer-causing mutations at the molecular level. The corresponding BRCA1-RING domain is on family zf-C3HC4_2, pfam13923.


Pssm-ID: 434253 [Multi-domain]  Cd Length: 65  Bit Score: 38.49  E-value: 1.10e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 341941803   282 AHFVKSISCQICEHILADPV-ETSCKHLFCRICILRCLkvmGSYCPSCRYPCFPTDLE 338
Cdd:pfam14835    2 DRLEKLLRCSRCTNILREPVcLGGCEHIFCSNCVSDCI---GTGCPVCYTPAWIQDLK 56
RING-HC_LONFs_rpt1 cd16513
first RING finger, HC subclass, found in the LON peptidase N-terminal domain and RING finger ...
289-329 1.14e-03

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: 37.67  E-value: 1.14e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 341941803  289 SCQICEHILADPVETSCKHLFCRICILRCLKvmgSYCPSCR 329
Cdd:cd16513     4 SCPLCRGLLFEPVTLPCGHTFCKRCLERDPS---SRCRLCR 41
RING-HC_TRY3-like cd23137
RING finger, HC subclass, found in Candida albicans transcriptional regulator of yeast form ...
289-331 1.53e-03

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: 37.45  E-value: 1.53e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 341941803  289 SCQICEHILADPVETSCKHLFCRICILRCLKVMGSYCPSCRYP 331
Cdd:cd23137     4 ACPICMNVAWKPVRLECSHVFCLRCLVKAQKQKKDNCPLCRAK 46
zf-RING_2 pfam13639
Ring finger domain;
288-329 1.65e-03

Ring finger domain;


Pssm-ID: 433370 [Multi-domain]  Cd Length: 44  Bit Score: 37.00  E-value: 1.65e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 341941803   288 ISCQICE---HILADPVETSCKHLFCRICILRCLKvMGSYCPSCR 329
Cdd:pfam13639    1 DECPICLeefEEGDKVVVLPCGHHFHRECLDKWLR-SSNTCPLCR 44
RING-HC_ORTHRUS_rpt2 cd23139
second RING finger, HC subclass, found in Arabidopsis thaliana ORTHRUS and similar proteins; ...
286-314 1.66e-03

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: 38.21  E-value: 1.66e-03
                          10        20
                  ....*....|....*....|....*....
gi 341941803  286 KSISCQICEHILADPVETSCKHLFCRICI 314
Cdd:cd23139     4 KEFGCQICKKVLSLPVSTPCGHNFCKACL 32
RING-HC_TRIM31_C-V cd16582
RING finger, HC subclass, found in tripartite motif-containing protein 31 (TRIM31) and similar ...
288-328 2.07e-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: 36.73  E-value: 2.07e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 341941803  288 ISCQICEHILADPVETSCKHLFCRICILRCLKVMGSY--CPSC 328
Cdd:cd16582     2 VICPICLDILQKPVTIDCGHNFCLQCITQIGETSCGFfkCPLC 44
RING-HC_RNF113A_B cd16539
RING finger, HC subclass, found in RING finger proteins RNF113A, RNF113B, and similar proteins; ...
290-329 2.22e-03

RING finger, HC subclass, found in RING finger proteins RNF113A, RNF113B, and similar proteins; RNF113A, also known as zinc finger protein 183 (ZNF183), is an E3 ubiquitin-protein ligase that physically interacts with the E2 protein, UBE2U. A nonsense mutation in RNF113A is associated with an X-linked trichothiodystrophy (TTD). Its yeast ortholog Cwc24p is predicted to have a spliceosome function and acts in a complex with Cef1p to participate in pre-U3 snoRNA splicing, indirectly affecting pre-rRNA processing. It is also important for the U2 snRNP binding to primary transcripts and co-migrates with spliceosomes. Moreover, the ortholog of RNF113A in fruit flies may also act as a spliceosome and is hypothesized to be involved in splicing, namely within the central nervous system. The ortholog in Caenorhabditis elegans is involved in DNA repair of inter-strand crosslinks. RNF113B, also known as zinc finger protein 183-like 1, shows high sequence similarity with RNF113A. Both RNF113A and RNF113B contain a CCCH-type zinc finger, which is commonly found in RNA-binding proteins involved in splicing, and a C3HC4-type RING-HC finger, which is frequently found in E3 ubiquitin ligases.


Pssm-ID: 438201 [Multi-domain]  Cd Length: 54  Bit Score: 37.19  E-value: 2.22e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 341941803  290 CQICEHILADPVETSCKHLFCRICILRCLKvMGSYCPSCR 329
Cdd:cd16539     8 CFICRKPFKNPVVTKCGHYFCEKCALKHYR-KSKKCFVCG 46
RING-HC_RNFT1-like cd16532
RING finger, HC subclass, found in RING finger and transmembrane domain-containing protein ...
289-329 3.07e-03

RING finger, HC subclass, found in RING finger and transmembrane domain-containing protein RNFT1, RNFT2, and similar proteins; Both RNFT1 and RNFT2 are multi-pass membrane proteins containing a C3HC4-type RING-HC finger. Their biological roles remain unclear.


Pssm-ID: 438194 [Multi-domain]  Cd Length: 41  Bit Score: 36.13  E-value: 3.07e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 341941803  289 SCQICEHILADPVETSCKHLFCRICILRCLKVMGSyCPSCR 329
Cdd:cd16532     2 ICPICQDEFKDPVVLRCKHIFCEDCVSEWFERERT-CPLCR 41
RING-HC_RNF222 cd16564
RING finger, HC subclass, found in RING finger protein 222 (RNF222) and similar proteins; ...
289-333 3.07e-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: 36.61  E-value: 3.07e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 341941803  289 SCQICEHILAD-PVETSCKHLFCRICILRCLKVMGSYCPSCRYPCF 333
Cdd:cd16564     2 ECPVCYEDFDDaPRILSCGHSFCEDCLVKQLVSMTISCPICRRVTF 47
RING-HC_RNF10 cd16536
RING finger, HC subclass, found in RING finger protein 10 (RNF10) and similar proteins; RNF10 ...
288-328 3.66e-03

RING finger, HC subclass, found in RING finger protein 10 (RNF10) and similar proteins; RNF10 is an E3 ubiquitin-protein ligase that interacts with mesenchyme Homeobox 2 (MEOX2) transcription factor, a regulator of the proliferation, differentiation and migration of vascular smooth muscle cells and cardiomyocytes; it enhances Meox2 activation of the p21 promoter. It also regulates the expression of myelin-associated glycoprotein (MAG) genes and is required for myelin production in Schwann cells of the peripheral nervous system. Moreover, RNF10 regulates retinoic acid-induced neuronal differentiation and the cell cycle exit of P19 embryonic carcinoma cells. RNF10 contains a C3HC4-type RING-HC finger and three putative nuclear localization signals.


Pssm-ID: 438198 [Multi-domain]  Cd Length: 54  Bit Score: 36.45  E-value: 3.66e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 341941803  288 ISCQICehiLADPVE---TSCKHLFCRICILRCLKVMGSY---CPSC 328
Cdd:cd16536     1 PQCPIC---LEPPVApriTRCGHIFCWPCILRYLSLSEKKwrkCPIC 44
RING-HC_BAR cd16497
RING finger, HC subclass, found in bifunctional apoptosis regulator (BAR); BAR, also known as ...
287-329 4.11e-03

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: 36.33  E-value: 4.11e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 341941803  287 SISCQICEHILADPVETSCKHLFCRICILRCLKV-MGSYCPSCR 329
Cdd:cd16497     1 EFLCHCCYDLLVNPTTLNCGHSFCRHCLALWWKSsKKTECPECR 44
RING-HC_CHR27-like cd23142
RING finger, HC subclass, found in Arabidopsis thaliana protein CHROMATIN REMODELING 27 (CHR27) ...
290-329 4.16e-03

RING finger, HC subclass, found in Arabidopsis thaliana protein CHROMATIN REMODELING 27 (CHR27) and similar proteins; CHR27, also called protein SNF2-RING-HELICASE-LIKE 1, is a probable helicase-like transcription factor involved in transcriptional gene silencing. It associates with SUVR2 and contributes to transcriptional gene silencing at RNA-directed DNA methylation (RdDM) target loci but also at RdDM-independent target loci. It may be involved in nucleosome positioning to form ordered nucleosome arrays on chromatin. It associates with SUVR2 and functions redundantly with FRG2. It is required for the efficient methylation of a broad range of RdDM target loci. CHR27 contains a typical C3HC4-type RING-HC finger.


Pssm-ID: 438504 [Multi-domain]  Cd Length: 55  Bit Score: 36.40  E-value: 4.16e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 341941803  290 CQICEHILADPVETSCKHLFCRICILRCLKVMGS-----YCPSCR 329
Cdd:cd23142     3 CPICNDPPEDAVVTLCGHVFCCECVFQYLSSDRTcrqfnHCPLCR 47
mRING-C3HGC3_RFWD3 cd16450
Modified RING finger, C3HGC3-type, found in RING finger and WD repeat domain-containing ...
286-337 4.30e-03

Modified RING finger, C3HGC3-type, found in RING finger and WD repeat domain-containing protein 3 (RFWD3) and similar proteins; RFWD3, also known as RING finger protein 201 (RNF201) or FLJ10520, is an E3 ubiquitin-protein ligase that forms a complex with Mdm2 and p53 to synergistically ubiquitinate p53 and acts as a positive regulator of p53 stability in response to DNA damage. It is phosphorylated by checkpoint kinase ATM/ATR and the phosphorylation mutant fails to stimulate p53 ubiquitination. RFWD3 also functions as a novel replication protein A (RPA)-associated protein involved in DNA replication checkpoint control. RFWD3 contains an N-terminal SQ-rich region followed by a RING finger domain that exhibits robust E3 ubiquitin ligase activity toward p53, a coiled-coil domain and three WD40 repeats in the C-terminus, the latter two of which may be responsible for protein-protein interaction. The RING finger in this family is a modified C3HGC3-type RING finger, but not a canonical C3H2C3-type RING-H2 finger or C3HC4-type RING-HC finger.


Pssm-ID: 438114 [Multi-domain]  Cd Length: 61  Bit Score: 36.44  E-value: 4.30e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 341941803  286 KSISCQIC--------EHILadpVETSCKHLFCRICILRCLKVMGSYCPSCRYPCFPTDL 337
Cdd:cd16450     1 EGNTCPICfepwtssgEHRL---VSLKCGHLFGYSCIEKWLKGKGKKCPQCNKKAKRSDI 57
RING-HC_ORTHRUS_rpt1 cd23138
first RING finger, HC subclass, found in Arabidopsis thaliana ORTHRUS and similar proteins; ...
287-334 4.60e-03

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: 35.88  E-value: 4.60e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 341941803  287 SISCQICEHILADPVETSCKHLFCRICILRCLKVMGSYCPSCRYPcFP 334
Cdd:cd23138     2 ELNCSFCMQLPERPVTTPCGHNFCLKCFQKWMGQGKKTCGTCRSP-IP 48
RING-HC_LNX4 cd16719
RING finger, HC subclass, found in ligand of numb protein X 4 (LNX4); LNX4, also known as PDZ ...
288-315 4.85e-03

RING finger, HC subclass, found in ligand of numb protein X 4 (LNX4); LNX4, also known as PDZ domain-containing RING finger protein 4 (PDZRN4), or SEMACAP3-like protein (SEMCAP3L), is an E3 ubiquitin-protein ligase responsible for the ubiquitination and degradation of Numb, a component of the Notch signaling pathway that functions in the specification of cell fates during development and is known to control cell numbers during neurogenesis in vertebrates. LNX4 contains an N-terminal C3HC4-type RING-HC finger, two PDZ domains, and a C-terminal LNX3 homology (LNX3H) domain.


Pssm-ID: 438379 [Multi-domain]  Cd Length: 53  Bit Score: 36.06  E-value: 4.85e-03
                          10        20
                  ....*....|....*....|....*...
gi 341941803  288 ISCQICEHILADPVETSCKHLFCRICIL 315
Cdd:cd16719     5 LKCKLCGKVLEEPLSTPCGHVFCAGCLL 32
mRING-HC-C3HC3D_LNX1 cd16779
Modified RING finger, HC subclass (C3HC3D-type), found in ligand of numb protein X 1 (LNX1); ...
290-329 5.10e-03

Modified RING finger, HC subclass (C3HC3D-type), found in ligand of numb protein X 1 (LNX1); LNX1, also known as numb-binding protein 1 or PDZ domain-containing RING finger protein 2, is a PDZ domain-containing RING-type E3 ubiquitin ligase responsible for the ubiquitination and degradation of Numb, a component of the Notch signaling pathway that functions in the specification of cell fates during development and is known to control cell numbers during neurogenesis in vertebrates. LNX1 contains an N-terminal modified C3HC3D-type RING-HC finger, a NPAY motif for Numb-LNX interaction, and four PDZ domains necessary for the binding of substrates, including CAR, ErbB2, SKIP, JAM4, CAST, c-Src, Claudins, RhoC, KCNA4, PAK6, PLEKHG5, PKC-alpha1, TYK2, PDZ-binding kinase (PBK), LNX2, and itself.


Pssm-ID: 438435 [Multi-domain]  Cd Length: 42  Bit Score: 35.94  E-value: 5.10e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 341941803  290 CQICEHILADPVETSCKHLFCRICILRCLkVMGSYCPSCR 329
Cdd:cd16779     4 CHICLQALIQPLDTPCGHTYCTLCLTNFL-VEKDFCPMDR 42
RING-HC_RNF146 cd16546
RING finger, HC subclass, found in RING finger protein 146 (RNF146) and similar proteins; ...
288-337 6.02e-03

RING finger, HC subclass, found in RING finger protein 146 (RNF146) and similar proteins; RNF146, also known as dactylidin, or iduna, is a cytoplasmic E3 ubiquitin-protein ligase that is responsible for PARylation-dependent ubiquitination (PARdU). It displays neuroprotective property due to its inhibition of Parthanatos, a PAR dependent cell death, via binding with Poly(ADP-ribose) (PAR). It also modulates PAR polymerase-1 (PARP-1)-mediated oxidative cell injury in cardiac myocytes. Moreover, RNF146 mediates tankyrase-dependent degradation of axin, thereby positively regulating Wnt signaling. It also facilitates DNA repair and protects against cell death induced by DNA damaging agents or gamma-irradiation by translocating to the nucleus after cellular injury and promoting the ubiquitination and degradation of various nuclear proteins involved in DNA damage repair. Furthermore, RNF146 is implicated in neurodegenerative disease and cancer development. It regulates the development and progression of non-small cell lung cancer (NSCLC) by enhancing cell growth, invasion, and survival. RNF146 contains an N-terminal C3HC4-type RING-HC finger followed by a WWE domain with a poly(ADP-ribose) (PAR) binding motif at the tail.


Pssm-ID: 438208 [Multi-domain]  Cd Length: 50  Bit Score: 35.82  E-value: 6.02e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 341941803  288 ISCQICEHILADPVETSCKHLFCRICIlRCLKVMGSYCPSCRYPcFPTDL 337
Cdd:cd16546     1 PECPICLQTCIHPVKLPCGHIFCYLCV-KGVAWQSKRCALCRQE-IPEDF 48
RING-HC_BAH1-like cd23127
RING finger, HC subclass, found in Arabidopsis thaliana protein BENZOIC ACID HYPERSENSITIVE 1 ...
287-329 6.99e-03

RING finger, HC subclass, found in Arabidopsis thaliana protein BENZOIC ACID HYPERSENSITIVE 1 (BAH1) and similar proteins; This subfamily includes Arabidopsis thaliana BAH1 and BAH1-like. BAH1, also known as protein NITROGEN LIMITATION ADAPTATION (NLA), or RING-type E3 ubiquitin transferase BAH1, acts as an E3 ubiquitin-protein ligase that mediates E2-dependent protein ubiquitination. It plays a role in salicylic acid-mediated negative feedback regulation of salicylic acid (SA) accumulation. It may be involved in the overall regulation of SA, benzoic acid and phenylpropanoid biosynthesis. It controls the adaptability to nitrogen limitation by channeling the phenylpropanoid metabolic flux to the induced anthocyanin synthesis. BAH1-like, also known as RING finger protein 178, or RING-type E3 ubiquitin transferase BAH1-like, is a probable E3 ubiquitin-protein ligase. Members of this subfamily contain a typical C3HC4-type RING-HC finger.


Pssm-ID: 438489 [Multi-domain]  Cd Length: 74  Bit Score: 36.22  E-value: 6.99e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 341941803  287 SISCQICEHILADPVETSCKHLFCRICILRCLKVMG----------SYCPSCR 329
Cdd:cd23127     8 DLTCSICLDTVFDPVALGCGHLFCNSCACSAASVLIfqglkaappeAKCPLCR 60
RING-HC_PEX10 cd16527
RING finger, HC subclass, found in peroxin-10 (PEX10) and similar proteins; PEX10, also known ...
290-337 7.06e-03

RING finger, HC subclass, found in peroxin-10 (PEX10) and similar proteins; PEX10, also known as peroxisome biogenesis factor 10, peroxisomal biogenesis factor 10, peroxisome assembly protein 10, or RING finger protein 69 (RNF69), is an integral peroxisomal membrane protein with two transmembrane regions and a C3HC4-type RING-HC finger within its cytoplasmically exposed C-terminus. It plays an essential role in peroxisome assembly, import of target substrates, and recycling or degradation of protein complexes and amino acids. It is an essential component of the spinal locomotor circuit, and thus its mutations may be involved in peroxisomal biogenesis disorders (PBD). Mutations in human PEX10 also result in autosomal recessive ataxia. Moreover, PEX10 functions as an E3-ubiquitin ligase with an E2, UBCH5C. It mono- or poly-ubiquitinates PEX5, a key player in peroxisomal matrix protein import, in a UBC4-dependent manner, to control PEX5 receptor recycling or degradation. It also links the E2 ubiquitin conjugating enzyme PEX4 to the protein import machinery of the peroxisome.


Pssm-ID: 438190 [Multi-domain]  Cd Length: 52  Bit Score: 35.67  E-value: 7.06e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 341941803  290 CQICEHILADPVETSCKHLFCRICILRCLkVMGSYCPSCRYPCFPTDL 337
Cdd:cd16527     3 CSLCLEERRHPTATPCGHLFCWSCITEWC-NEKPECPLCREPFQPQRL 49
RING-HC_LNX3-like cd16512
RING finger, HC subclass, found in ligand of Numb protein LNX3, LNX4, and similar proteins; ...
290-315 8.82e-03

RING finger, HC subclass, found in ligand of Numb protein LNX3, LNX4, and similar proteins; The ligand of Numb protein X (LNX) family, also known as PDZ and RING (PDZRN) family, includes LNX1-5, which can interact with Numb, a key regulator of neurogenesis and neuronal differentiation. LNX5 (also known as PDZK4, or PDZRN4L) shows high sequence homology to LNX3 and LNX4, but it lacks the RING domain. LNX1-4 proteins function as E3 ubiquitin ligases and have a unique domain architecture consisting of an N-terminal RING-HC finger for E3 ubiquitin ligase activity and either two or four PDZ domains necessary for the substrate-binding. This family corresponds to LNX3/LNX4-like proteins, which contains a C3HC4-type RING-HC finger and two PDZ domains.


Pssm-ID: 438175 [Multi-domain]  Cd Length: 43  Bit Score: 35.08  E-value: 8.82e-03
                          10        20
                  ....*....|....*....|....*.
gi 341941803  290 CQICEHILADPVETSCKHLFCRICIL 315
Cdd:cd16512     3 CKLCLGVLEEPLATPCGHVFCAGCVL 28
 
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.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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