Pex2 / Pex12 amino terminal region; This region is found at the N terminal of a number of known and predicted peroxins including Pex2, Pex10 and Pex12. This conserved region is usually associated with a C terminal ring finger (pfam00097) domain.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 672041881   64 KALEQLVWSQFTQCFHGFKPGLLA-RFEPEVKAFLWLFLWRFTIYSKNATVGQSVLNIQYKNDSSPnpvYQPPSKNQKLL 142
Cdd:pfam04757   2 EELESLLRPQLRYILRLLAGQRFPlNYFDEIKLLLDLLYFRLTLLRGNATLGEEYYGLKRVSDRDG---GRLLSRRRRLL 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 672041881  143 YAVCTIGGRWLEERCYDLF--------RNRHLASFGKAK------QCMNFVVGLLKLGELMNFLIFLqKGKFATLTERLL 208
Cdd:pfam04757  79 SLLLLVLLPYLLRKLDSLLprlsandlESRNARDSLKSRlkryllKLYPFLESLYKLLNLHLFLFYL-TGKYYSLSKRLL 157

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 672041881  209 GIHSVFCKPQSM----REVGFEymnrELLWHGFAEFLVFLLPLINIQKLKAKLSSWC 261
Cdd:pfam04757 158 GIRYVRLKPLDIfsneRRVSYE----QLLWNAFSELLGFLLPLLLAVILFLKLLEWW 210

Pex2 / Pex12 amino terminal region; This region is found at the N terminal of a number of known and predicted peroxins including Pex2, Pex10 and Pex12. This conserved region is usually associated with a C terminal ring finger (pfam00097) domain.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 672041881   64 KALEQLVWSQFTQCFHGFKPGLLA-RFEPEVKAFLWLFLWRFTIYSKNATVGQSVLNIQYKNDSSPnpvYQPPSKNQKLL 142
Cdd:pfam04757   2 EELESLLRPQLRYILRLLAGQRFPlNYFDEIKLLLDLLYFRLTLLRGNATLGEEYYGLKRVSDRDG---GRLLSRRRRLL 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 672041881  143 YAVCTIGGRWLEERCYDLF--------RNRHLASFGKAK------QCMNFVVGLLKLGELMNFLIFLqKGKFATLTERLL 208
Cdd:pfam04757  79 SLLLLVLLPYLLRKLDSLLprlsandlESRNARDSLKSRlkryllKLYPFLESLYKLLNLHLFLFYL-TGKYYSLSKRLL 157

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 672041881  209 GIHSVFCKPQSM----REVGFEymnrELLWHGFAEFLVFLLPLINIQKLKAKLSSWC 261
Cdd:pfam04757 158 GIRYVRLKPLDIfsneRRVSYE----QLLWNAFSELLGFLLPLLLAVILFLKLLEWW 210

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.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 672041881  281 CALCGEWPTMPHTI-GCEHVFCYYCVKSSfLFDMYFTCPKC 320
Cdd:pfam00097   1 CPICLEEPKDPVTLlPCGHLFCSKCIRSW-LESGNVTCPLC 40

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

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 672041881 280 ECALCGEWPTMPHTIGCEHVFCYYCVKSSFLFDMYFTCPKCGTEVH 325
Cdd:COG5574  217 KCFLCLEEPEVPSCTPCGHLFCLSCLLISWTKKKYEFCPLCRAKVY 262

Pex2 / Pex12 amino terminal region; This region is found at the N terminal of a number of known and predicted peroxins including Pex2, Pex10 and Pex12. This conserved region is usually associated with a C terminal ring finger (pfam00097) domain.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 672041881   64 KALEQLVWSQFTQCFHGFKPGLLA-RFEPEVKAFLWLFLWRFTIYSKNATVGQSVLNIQYKNDSSPnpvYQPPSKNQKLL 142
Cdd:pfam04757   2 EELESLLRPQLRYILRLLAGQRFPlNYFDEIKLLLDLLYFRLTLLRGNATLGEEYYGLKRVSDRDG---GRLLSRRRRLL 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 672041881  143 YAVCTIGGRWLEERCYDLF--------RNRHLASFGKAK------QCMNFVVGLLKLGELMNFLIFLqKGKFATLTERLL 208
Cdd:pfam04757  79 SLLLLVLLPYLLRKLDSLLprlsandlESRNARDSLKSRlkryllKLYPFLESLYKLLNLHLFLFYL-TGKYYSLSKRLL 157

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 672041881  209 GIHSVFCKPQSM----REVGFEymnrELLWHGFAEFLVFLLPLINIQKLKAKLSSWC 261
Cdd:pfam04757 158 GIRYVRLKPLDIfsneRRVSYE----QLLWNAFSELLGFLLPLLLAVILFLKLLEWW 210

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.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 672041881  281 CALCGEWPTMPHTI-GCEHVFCYYCVKSSfLFDMYFTCPKC 320
Cdd:pfam00097   1 CPICLEEPKDPVTLlPCGHLFCSKCIRSW-LESGNVTCPLC 40

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.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 672041881 281 CALCGEWPTMPHTIG-CEHVFCYYCVKSSFLFDMYftCPKCGTEVHSVQPLKS 332
Cdd:cd16737   13 CRICKGYLIKPTTVTeCLHTFCKSCIVQHFEDSND--CPECGIQVHETNPLEM 63

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.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 672041881 280 ECALCGEWPTMPHTIGCEHVFCYYCVKSSFLFDMYfTCPKCGTEVHS 326
Cdd:cd16542    3 DCAVCLEVLHQPVRTRCGHVFCRPCIATSLRNNTW-TCPYCRAYLSS 48

RING finger found in polycomb group RING finger protein 2 (PCGF2) and similar proteins; PCGF2, also known as DNA-binding protein Mel-18, RING finger protein 110 (RNF110), or zinc finger protein 144 (ZNF144), is one of six PcG RING finger (PCGF) homologs (PCGF1/NSPc1, PCGF2/Mel-18, PCGF3, PCGF4/BMI1, PCGF5, and PCGF6/MBLR). It serves as the core component of a canonical Polycomb repressive complex 1 (PRC1), which is composed of a chromodomain-containing protein (CBX2, CBX4, CBX6, CBX7 or CBX8) and a Polyhomeotic protein (PHC1, PHC2, or PHC3). Like other PCGF homologs, PCGF2 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. Moreover, PCGF2 uniquely regulates PRC1 to specify mesoderm cell fate in embryonic stem cells. It is required for PRC1 stability and maintenance of gene repression in embryonic stem cells (ESCs) and essential for ESC differentiation into early cardiac-mesoderm precursors. PCGF2 also plays a significant role in the angiogenic function of endothelial cells (ECs) by regulating endothelial gene expression. Furthermore, PCGF2 is a SUMO-dependent regulator of hormone receptors. It facilitates the deSUMOylation process by inhibiting PCGF4/BMI1-mediated ubiquitin-proteasomal degradation of SUMO1/sentrin-specific protease 1 (SENP1). It is also a novel negative regulator of breast cancer stem cells (CSCs) that inhibits the stem cell population and in vitro and in vivo self-renewal through the inactivation of Wnt-mediated Notch signaling. PCGF2 contains a C3HC4-type RING-HC finger.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 672041881 281 CALCGEWPTMPHTI-GCEHVFCYYCVKSSFLFDMYftCPKCGTEVHSVQPLKS 332
Cdd:cd16734   17 CALCGGYFIDAATIvECLHSFCKTCIVRYLETNKY--CPMCDVQVHKTRPLLS 67

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.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 672041881 281 CALCGEWPTMPHTIGCEHVFCYYCVKSSFL-FDMYFTCPKC 320
Cdd:cd16601    4 CSLCKEYLKDPVIIECGHNFCRACITRFWEeLDGDFPCPQC 44

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.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 672041881 280 ECALCGEWPTMPHTIGCEHVFCYYCVKSSFLFDMyfTCPKCGTEV 324
Cdd:cd16546    2 ECPICLQTCIHPVKLPCGHIFCYLCVKGVAWQSK--RCALCRQEI 44

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.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 672041881 280 ECALCGEWPTMPHTIGCEHVFCYYCVKSSFLFDMYFTCPKCGTEV 324
Cdd:cd16568    6 ECIICHEYLYEPMVTTCGHTYCYTCLNTWFKSNRSLSCPDCRTKI 50

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.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 672041881 281 CALCGEWPTMPHTIGCEHVFCYYCV----KSSFLFDMYFTCPKCGTEV 324
Cdd:cd23142    3 CPICNDPPEDAVVTLCGHVFCCECVfqylSSDRTCRQFNHCPLCRQKL 50

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.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 672041881 281 CALCGEWPTMPHTIGCEHVFCYYCVKSSFLFDMY--FTCPKC 320
Cdd:cd16609    6 CSICLGLYQDPVTLPCQHSFCRACIEDHWRQKDEgsFSCPEC 47

RING finger, HC subclass, found in polycomb group RING finger protein 1 (PCGF1) and similar proteins; PCGF1, also known as nervous system Polycomb-1 (NSPc1) or RING finger protein 68 (RNF68), is one of six PcG RING finger (PCGF) homologs (PCGF1/NSPc1, PCGF2/Mel-18, PCGF3, PCGF4/BMI1, PCGF5, and PCGF6/MBLR). It serves as the core component of a noncanonical Polycomb repressive complex 1 (PRC1)-like BCOR complex that also contains RING1, RNF2, RYBP, SKP1, as well as the BCL6 co-repressor BCOR and the histone demethylase KDM2B, and is required to maintain the transcriptionally repressive state of some genes, such as Hox genes, BCL6 and the cyclin-dependent kinase inhibitor, CDKN1A. PCGF1 promotes cell cycle progression and enhances cell proliferation as well. It is a cell growth regulator that acts as a transcriptional repressor of p21Waf1/Cip1 via the retinoid acid response element (RARE element). Moreover, PCGF1 functions as an epigenetic regulator involved in hematopoietic cell differentiation. It cooperates with the transcription factor runt-related transcription factor 1 (Runx1) in regulating differentiation and self-renewal of hematopoietic cells. Furthermore, PCGF1 represents a physical and functional link between Polycomb function and pluripotency. PCGF1 contains a C3HC4-type RING-HC finger.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 672041881 281 CALCGEWPTMPHTIG-CEHVFCYYCVKSSFLFDMYftCPKCGTEVHSVQPL 330
Cdd:cd16733   12 CYLCAGYFIDATTITeCLHTFCKSCIVKYLQTSKY--CPMCNIKIHETQPL 60