RING finger, H2 subclass, found in vacuolar protein sorting-associated protein 11 homolog (Vps11) and similar proteins; Vps11, also known as RING finger protein 108 (RNF108), is a soluble protein involved in regulation of glycolipid degradation and retrograde toxin transport. It is highly expressed in heart and pancreas. Vps11 associates with Vps16, Vps18, and Vps33 to form a Class C Vps core complex that is required for soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNARE)-mediated membrane fusion at the lysosome-like yeast vacuole. The core complex, together with two additional compartment-specific subunits, forms the tethering complexes HOPS (homotypic vacuole fusion and protein sorting) and CORVET (class C core vacuole/endosome transport). CORVET contains the additional Vps3 and Vps8 subunits. It operates at endosomes, controls traffic into late endosomes and interacts with the Rab5/Vps21-GTP form. HOPS contains the additional Vps39 and Vps41 subunits. It operates at the lysosomal vacuole, controls all traffic from late endosomes into the vacuole and interacts with the Rab7/Ypt7-GTP form. Vps11 is a central scaffold protein upon which both HOPS and CORVET assemble. The HOPS and CORVET complexes disassemble in the absence of Vps11, resulting in massive fragmentation of vacuoles. Vps11 contains a clathrin repeat domain and a C-terminal C3H2C3-type RING-H2 finger. This subfamily also includes Vps11 homologs found in fungi, such as Saccharomyces cerevisiae vacuolar membrane protein Pep5p, also known as carboxypeptidase Y-deficient protein 5, vacuolar morphogenesis protein 1, or vacuolar biogenesis protein END1. Pep5p is essential for vacuolar biogenesis. It associates with Pep3p to form a core Pep3p/Pep5p complex that promotes vesicular docking/fusion reactions in conjunction with SNARE proteins at multiple steps in transport routes to the vacuole.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1804891953 815 TKCSICNSALELPSVHFLCGHSFHQHCFESYSESDADCPTCLPE 858
Cdd:cd16688     1 TKCSACGSTLDLPSVHFLCGHSFHQHCLEDYEENDRECPLCAPE 44

Region in Clathrin and VPS; Each region is about 140 amino acids long. The regions are composed of multiple alpha helical repeats. They occur in the arm region of the Clathrin heavy chain.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1804891953 412 KLEPSYVIRKFLDAQRIHNLTAYLQT-LHRQSLANADHTTLLLNCYTKLKDSSKLEEFIKKKSesevHFDVETAIKVLRQ 490
Cdd:pfam00637   7 PIDVSRVVKLFEKAGLLEELISYLESaLKEDSRENPALQTALIELYAKYDDPEELEEFLKKNN----NYDLEKVAKLCEK 82

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 1804891953 491 AGYYSHALYLaenHAHHEWYLK-IQL-EDIKNYQEALRYIGKL 531
Cdd:pfam00637  83 ADLYEEAVIL---YKKIGNWKEaISLlKKLGDYKDAIEYAVKS 122

RING finger, H2 subclass, found in vacuolar protein sorting-associated protein 11 homolog (Vps11) and similar proteins; Vps11, also known as RING finger protein 108 (RNF108), is a soluble protein involved in regulation of glycolipid degradation and retrograde toxin transport. It is highly expressed in heart and pancreas. Vps11 associates with Vps16, Vps18, and Vps33 to form a Class C Vps core complex that is required for soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNARE)-mediated membrane fusion at the lysosome-like yeast vacuole. The core complex, together with two additional compartment-specific subunits, forms the tethering complexes HOPS (homotypic vacuole fusion and protein sorting) and CORVET (class C core vacuole/endosome transport). CORVET contains the additional Vps3 and Vps8 subunits. It operates at endosomes, controls traffic into late endosomes and interacts with the Rab5/Vps21-GTP form. HOPS contains the additional Vps39 and Vps41 subunits. It operates at the lysosomal vacuole, controls all traffic from late endosomes into the vacuole and interacts with the Rab7/Ypt7-GTP form. Vps11 is a central scaffold protein upon which both HOPS and CORVET assemble. The HOPS and CORVET complexes disassemble in the absence of Vps11, resulting in massive fragmentation of vacuoles. Vps11 contains a clathrin repeat domain and a C-terminal C3H2C3-type RING-H2 finger. This subfamily also includes Vps11 homologs found in fungi, such as Saccharomyces cerevisiae vacuolar membrane protein Pep5p, also known as carboxypeptidase Y-deficient protein 5, vacuolar morphogenesis protein 1, or vacuolar biogenesis protein END1. Pep5p is essential for vacuolar biogenesis. It associates with Pep3p to form a core Pep3p/Pep5p complex that promotes vesicular docking/fusion reactions in conjunction with SNARE proteins at multiple steps in transport routes to the vacuole.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1804891953 815 TKCSICNSALELPSVHFLCGHSFHQHCFESYSESDADCPTCLPE 858
Cdd:cd16688     1 TKCSACGSTLDLPSVHFLCGHSFHQHCLEDYEENDRECPLCAPE 44

Region in Clathrin and VPS; Each region is about 140 amino acids long. The regions are composed of multiple alpha helical repeats. They occur in the arm region of the Clathrin heavy chain.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1804891953 412 KLEPSYVIRKFLDAQRIHNLTAYLQT-LHRQSLANADHTTLLLNCYTKLKDSSKLEEFIKKKSesevHFDVETAIKVLRQ 490
Cdd:pfam00637   7 PIDVSRVVKLFEKAGLLEELISYLESaLKEDSRENPALQTALIELYAKYDDPEELEEFLKKNN----NYDLEKVAKLCEK 82

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 1804891953 491 AGYYSHALYLaenHAHHEWYLK-IQL-EDIKNYQEALRYIGKL 531
Cdd:pfam00637  83 ADLYEEAVIL---YKKIGNWKEaISLlKKLGDYKDAIEYAVKS 122

Clathrin heavy chain repeat homology;

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1804891953  406 YIRTIGKLEPSYVIRKFLDAQRIHNLTAYLQTLHRQSLANADHTTLLLNCYTKlKDSSKLEEFIKKKSEsevHFDVETAI 485
Cdd:smart00299   1 LLEVSDPIDVSEVVELFEKRNLLEELIPYLESALKLNSENPALQTKLIELYAK-YDPQKEIERLDNKSN---HYDIEKVG 76

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*
gi 1804891953  486 KVLRQAGYYSHALYLAENHAHHEWYLKIQLEDIKNYQEALRYIGK 530
Cdd:smart00299  77 KLCEKAKLYEEAVELYKKDGNFKDAIVTLIEHLGNYEKAIEYFVK 121

Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal metal-binding domain [Cell wall/membrane/envelope biogenesis];

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1804891953 328 EDVVDVLAEWGSLYVLTRDgrvhalqekdtqtklenlFEMAINLAKSQHLDSDGLAQIFMQYGDHLYSKGNHDGAVQQYI 407
Cdd:COG2956   107 PDDAEALRLLAEIYEQEGD------------------WEKAIEVLERLLKLGPENAHAYCELAELYLEQGDYDEAIEALE 168

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1804891953 408 RTIgKLEPSYV------IRKFLDAQRIHNLTAYLQTLHRQSLANADHTTLLLNCYTKLKDSSKLEEFIKKKSESEVHFDV 481
Cdd:COG2956   169 KAL-KLDPDCArallllAELYLEQGDYEEAIAALERALEQDPDYLPALPRLAELYEKLGDPEEALELLRKALELDPSDDL 247

                         170       180
                  ....*....|....*....|....
gi 1804891953 482 ETAI-KVLRQAGYYSHALYLAENH 504
Cdd:COG2956   248 LLALaDLLERKEGLEAALALLERQ 271

RING finger, H2 subclass, found in vacuolar protein sorting-associated protein 11 homolog (Vps11) and similar proteins; Vps11, also known as RING finger protein 108 (RNF108), is a soluble protein involved in regulation of glycolipid degradation and retrograde toxin transport. It is highly expressed in heart and pancreas. Vps11 associates with Vps16, Vps18, and Vps33 to form a Class C Vps core complex that is required for soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNARE)-mediated membrane fusion at the lysosome-like yeast vacuole. The core complex, together with two additional compartment-specific subunits, forms the tethering complexes HOPS (homotypic vacuole fusion and protein sorting) and CORVET (class C core vacuole/endosome transport). CORVET contains the additional Vps3 and Vps8 subunits. It operates at endosomes, controls traffic into late endosomes and interacts with the Rab5/Vps21-GTP form. HOPS contains the additional Vps39 and Vps41 subunits. It operates at the lysosomal vacuole, controls all traffic from late endosomes into the vacuole and interacts with the Rab7/Ypt7-GTP form. Vps11 is a central scaffold protein upon which both HOPS and CORVET assemble. The HOPS and CORVET complexes disassemble in the absence of Vps11, resulting in massive fragmentation of vacuoles. Vps11 contains a clathrin repeat domain and a C-terminal C3H2C3-type RING-H2 finger. This subfamily also includes Vps11 homologs found in fungi, such as Saccharomyces cerevisiae vacuolar membrane protein Pep5p, also known as carboxypeptidase Y-deficient protein 5, vacuolar morphogenesis protein 1, or vacuolar biogenesis protein END1. Pep5p is essential for vacuolar biogenesis. It associates with Pep3p to form a core Pep3p/Pep5p complex that promotes vesicular docking/fusion reactions in conjunction with SNARE proteins at multiple steps in transport routes to the vacuole.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1804891953 815 TKCSICNSALELPSVHFLCGHSFHQHCFESYSESDADCPTCLPE 858
Cdd:cd16688     1 TKCSACGSTLDLPSVHFLCGHSFHQHCLEDYEENDRECPLCAPE 44

RING finger, H2 subclass, found in vacuolar protein sorting-associated proteins Vps8, Vps11, Vps18, Vps41, and similar proteins; This subfamily corresponds to a group of vacuolar protein sorting-associated proteins containing a C-terminal C3H2C3-type RING-H2 finger, which includes Vps8, Vps11, Vps18, and Vps41. Vps11 and Vps18 associate with Vps16 and Vps33 to form a Class C Vps core complex that is required for soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNARE)-mediated membrane fusion at the lysosome-like yeast vacuole. The core complex, together with two additional compartment-specific subunits, forms the tethering complexes HOPS (homotypic vacuole fusion and protein sorting) and CORVET (class C core vacuole/endosome transport). CORVET contains the additional Vps3 and Vps8 subunits. It operates at endosomes, controls traffic into late endosomes and interacts with the Rab5/Vps21-GTP form. HOPS contains the additional Vps39 and Vps41 subunits. It operates at the lysosomal vacuole, controls all traffic from late endosomes into the vacuole and interacts with the Rab7/Ypt7-GTP form.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1804891953 816 KCSICNSAL-------ELPSVHFLCGHSFHQHCFESYSESDADCPTCL 856
Cdd:cd16484     1 KCPICTLPLkesdvgaNSPVVVFFCGHMFHKFCLPELSMTEAACPICL 48

Zinc finger, C3HC4 type (RING finger);

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 1804891953 816 KCSICNSALELPSVHFLCGHSFHQHCFESYSESDADCPTC 855
Cdd:pfam13923   1 MCPICMDMLKDPSTTTPCGHVFCQDCILRALRAGNECPLC 40

Clathrin heavy chain repeat homology;

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1804891953  406 YIRTIGKLEPSYVIRKFLDAQRIHNLTAYLQTLHRQSLANADHTTLLLNCYTKlKDSSKLEEFIKKKSEsevHFDVETAI 485
Cdd:smart00299   1 LLEVSDPIDVSEVVELFEKRNLLEELIPYLESALKLNSENPALQTKLIELYAK-YDPQKEIERLDNKSN---HYDIEKVG 76

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*
gi 1804891953  486 KVLRQAGYYSHALYLAENHAHHEWYLKIQLEDIKNYQEALRYIGK 530
Cdd:smart00299  77 KLCEKAKLYEEAVELYKKDGNFKDAIVTLIEHLGNYEKAIEYFVK 121

RING finger, H2 subclass, found in Tetratricopeptide repeat protein 3 (TTC3) and similar proteins; TTC3, also known as protein DCRR1, TPR repeat protein D, TPR repeat protein 3, or RING finger protein 105 (RNF105), is an E3 ubiquitin-protein ligase encoded by a gene within the Down syndrome (DS) critical region on chromosome 21. It affects differentiation and Golgi compactness in neurons through specific actin-regulating pathways. It inhibits the neuronal-like differentiation of pheocromocytoma cells by activating RhoA and by binding to Citron proteins. TTC3 is an Akt-specific E3 ligase that binds to phosphorylated Akt and facilitates its ubiquitination and degradation within the nucleus. It contains four N-terminal TPR motifs, a potential coiled-coil region and a Citron binding region in the central part, and a C-terminal C3H2C2-type RING-H2 finger.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 1804891953 816 KCSICNSALELPSVHFL-CGHSFHQHCFESYSESDADCPTC 855
Cdd:cd16481     1 PCIICHDDLKPDQLAKLeCGHIFHKECIKQWLKEQSTCPTC 41

RING finger, H2 subclass, found in autocrine motility factor receptor (AMFR) and similar proteins; AMFR, also known as AMF receptor, or RING finger protein 45, or ER-protein gp78, is an internalizing cell surface glycoprotein localized in both plasma membrane caveolae and the endoplasmic reticulum (ER). It is involved in the regulation of cellular adhesion, proliferation, motility and apoptosis, as well as in the process of learning and memory. AMFR also functions as a RING finger-dependent ubiquitin protein ligase (E3) implicated in the degradation from the ER. AMFR contains an N-terminal RING-H2 finger and a C-terminal ubiquitin-associated (UBA)-like CUE domain.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1804891953 816 KCSIC----NSALELPsvhflCGHSFHQHCFESYSESDADCPTC 855
Cdd:cd16455     2 DCAICwesmQSARKLP-----CGHLFHNSCLRSWLEQDTSCPTC 40

RING finger, H2 subclass, found in synoviolin and similar proteins; Synoviolin, also known as synovial apoptosis inhibitor 1 (Syvn1), Hrd1, or Der3, is an endoplasmic reticulum (ER)-anchoring E3 ubiquitin ligase that functions as a suppressor of ER stress-induced apoptosis and plays a role in homeostasis maintenance. It also targets tumor suppressor gene p53 for proteasomal degradation, suggesting crosstalk between ER associated degradation (ERAD) and p53 mediated apoptotic pathway under ER stress. Moreover, synoviolin controls body weight and mitochondrial biogenesis through negative regulation of the thermogenic coactivator peroxisome proliferator-activated receptor coactivator (PGC)-1beta. It upregulates amyloid beta production by targeting a negative regulator of gamma-secretase, Retention in endoplasmic reticulum 1 (Rer1), for degradation. It is also involved in the degradation of endogenous immature nicastrin, and affects amyloid beta-protein generation. Moreover, synoviolin is highly expressed in rheumatoid synovial cells and may be involved in the pathogenesis of rheumatoid arthritis (RA). It functions as an anti-apoptotic factor that is responsible for the outgrowth of synovial cells during the development of RA. It promotes inositol-requiring enzyme 1 (IRE1) ubiquitination and degradation in synovial fibroblasts with collagen-induced arthritis. Furthermore, the upregulation of synoviolin may represent a protective response against neurodegeneration in Parkinson's disease (PD). In addition, synoviolin is involved in liver fibrogenesis. Synoviolin contains a C3H2C2-type RING-H2 finger.

                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 1804891953 817 CSICNSALELPSVHFLCGHSFHQHCFESYSESDADCPTC 855
Cdd:cd16479     4 CIICREEMTVGAKKLPCGHIFHLSCLRSWLQRQQTCPTC 42

RING finger, H2 subclass, found in Saccharomyces cerevisiae transmembrane E3 ubiquitin-protein ligase 1 (TUL1) and similar proteins; This subfamily includes Saccharomyces cerevisiae TUL1, Schizosaccharomyces pombe DSC E3 ubiquitin ligase complex subunit 1 (DSC1), and Arabidopsis thaliana protein FLYING SAUCER 2 (FLY2). TUL1 is the catalytic component of DSC E3 ubiquitin ligase complexes that tag proteins present in Golgi, endosome and vacuole membranes and function in protein homeostasis under non-stress conditions, and support a role in protein quality control. It mediates ubiquitination of vacuolar proteins such as CPS1, PPN1, PEP12 and other proteins containing exposed hydrophilic residues within their transmembrane domains, leading to their sorting into internal vesicles in late endosomes. TUL1 also targets the unpalmitoylated endosomal SNARE TLG1 to the multivesicular body (MVB) pathway. DSC1, also known as defective for SREBP cleavage protein 1, is the catalytic component of the DSC E3 ubiquitin ligase complex required for the sre1 transcriptional activator proteolytic cleavage to release the soluble transcription factor from the membrane in low oxygen or sterol conditions. FLY2 acts as an E3 ubiquitin-protein ligase that may be involved in xylem development. Members of this subfamily contain a C3H2C3-type RING-H2 finger.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1804891953 815 TKCSICNSALELPSVHFL--------CGHSFHQHCFESYSESDADCPTC 855
Cdd:cd23117     5 VDCVICMSDIELPSTNSVrrdymvtpCNHIFHTNCLERWMDIKLECPTC 53

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

                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 1804891953 817 CSICNSALELPSVHflCGHSFHQHCFESYSESDADCPTC 855
Cdd:pfam13445   1 CPICLELFTDPVLP--CGHTFCRECLEEMSQKKGGKFKC 37

RING finger, H2 subclass, found in RING finger proteins RNF111, RNF165, and similar proteins; The family includes RING finger proteins RNF111, RNF165, and similar proteins. RNF111, also known as Arkadia, is a nuclear E3 ubiquitin-protein ligase that targets intracellular effectors and modulators of transforming growth factor beta (TGF-beta)/Nodal-related signaling for polyubiquitination and proteasome-dependent degradation. It also interacts with the clathrin-adaptor 2 (AP2) complex and regulates endocytosis of certain cell surface receptors, leading to modulation of epidermal growth factor (EGF) and possibly other signaling pathways. The N-terminal half of RNF111 harbors three SUMO-interacting motifs (SIMs). It thus functions as a SUMO-targeted ubiquitin ligase (STUbL) that directly links nonproteolytic ubiquitylation and SUMOylation in the DNA damage response, as well as triggers degradation of signal-induced polysumoylated proteins, such as the promyelocytic leukemia protein (PML). RNF165, also known as Arkadia-like 2, Arkadia2, or Ark2C, is an E3 ubiquitin ligase with homology to the C-terminal half of RNF111. It is expressed specifically in the nervous system, and can serve to amplify neuronal responses to specific signals. It acts as a positive regulator of bone morphogenetic protein (BMP)-Smad signaling that is involved in motor neuron (MN) axon elongation. Both RNF165 and RNF111 contain a C-terminal C3H2C3-type RING-H2 finger.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1804891953 816 KCSICNSALE-------LPsvhflCGHSFHQHCFESYSESDADCPTC 855
Cdd:cd16474     2 KCTICLSDFEegedvrrLP-----CMHLFHQECVDQWLSTNKRCPIC 43

Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal metal-binding domain [Cell wall/membrane/envelope biogenesis];

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1804891953 328 EDVVDVLAEWGSLYVLTRDgrvhalqekdtqtklenlFEMAINLAKSQHLDSDGLAQIFMQYGDHLYSKGNHDGAVQQYI 407
Cdd:COG2956   107 PDDAEALRLLAEIYEQEGD------------------WEKAIEVLERLLKLGPENAHAYCELAELYLEQGDYDEAIEALE 168

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1804891953 408 RTIgKLEPSYV------IRKFLDAQRIHNLTAYLQTLHRQSLANADHTTLLLNCYTKLKDSSKLEEFIKKKSESEVHFDV 481
Cdd:COG2956   169 KAL-KLDPDCArallllAELYLEQGDYEEAIAALERALEQDPDYLPALPRLAELYEKLGDPEEALELLRKALELDPSDDL 247

                         170       180
                  ....*....|....*....|....
gi 1804891953 482 ETAI-KVLRQAGYYSHALYLAENH 504
Cdd:COG2956   248 LLALaDLLERKEGLEAALALLERQ 271

RING finger, H2 subclass, found in TRAF-interacting protein (TRAIP) and similar proteins; TRAIP, also known as RING finger protein 206 (RNF206) or TRIP, is a ubiquitously expressed nucleolar E3 ubiquitin ligase important for cellular proliferation and differentiation. It is found near mitotic chromosomes and functions as a regulator of the spindle assembly checkpoint. TRAIP interacts with tumor necrosis factor (TNF)-receptor-associated factor (TRAF) proteins and inhibits TNF-alpha-mediated nuclear factor (NF)-kappaB activation. It also interacts with two tumor suppressors CYLD and spleen tyrosine kinase (Syk), and DNA polymerase eta, which facilitates translesional synthesis after DNA damage. TRAIP contains an N-terminal C3H2C2-type RING-H2 finger and an extended coiled-coil domain.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1804891953 817 CSICN----SALELPSVHflCGHSFHQHCFESYSESDADCPTC 855
Cdd:cd16480     2 CTICSdffdNSRDVAAIH--CGHTFHYDCLLQWFDTSRTCPQC 42

WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1804891953 142 VVSCLTVHENLNFMAIGFTDGSVTLnkGDITRDRHSKTQILHKGnyPVTGLAFRQAGKTthLFVVTTEN-VQSYIVSgKD 220
Cdd:cd00200    11 GVTCVAFSPDGKLLATGSGDGTIKV--WDLETGELLRTLKGHTG--PVRDVAASADGTY--LASGSSDKtIRLWDLE-TG 83

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1804891953 221 YPRVELDTHGCGLRCSALsdpSQDLQFIVAG--DECVYLYQPDERGPCFAFEGHK-----LIAHWFRGYLIIVSRDRKV 292
Cdd:cd00200    84 ECVRTLTGHTSYVSSVAF---SPDGRILSSSsrDKTIKVWDVETGKCLTTLRGHTdwvnsVAFSPDGTFVASSSQDGTI 159

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.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 1804891953 816 KCSICNSALELPSVHFLCGHSFHQHCFESYSE-SDADCPTC 855
Cdd:cd16503     4 TCSICQDLLHDCVSLQPCMHNFCAACYSDWMErSNTECPTC 44

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.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1804891953 817 CSICNSALELPsVHFLCGHSFHQHCFESYSESD----ADCPTC 855
Cdd:cd16604     3 CPICLDLLKDP-VTLPCGHSFCMGCLGALWGAGrggrASCPLC 44

RING finger, H2 subclass, found in Saccharomyces cerevisiae vacuolar membrane protein PEP3 (Pep3p) and similar proteins; Pep3p, also known as carboxypeptidase Y-deficient protein 3, vacuolar morphogenesis protein 8, vacuolar protein sorting-associated protein 18 (Vps18p), or vacuolar protein-targeting protein 18, is a vacuolar membrane protein that affects late Golgi functions required for vacuolar protein sorting and efficient alpha-factor prohormone maturation. It is required for vacuolar biogenesis and for trafficking of hydrolase precursors to the vacuole. The disruption of PEP3 may cause hypersensitivity to heat shock and ethanol stresses, probably due to disappearance of normal vacuoles. As a component of the homotypic fusion and vacuole protein sorting (HOPS) and class C core vacuole/endosome tethering (CORVET) complexes, its overexpression shortens lag phase but does not alter growth rate in Saccharomyces cerevisiae exposed to acetic acid stress. Moreover, Pep3p forms the Class C Vps protein complex (C-Vps complex) with Pep5p (also known as Vps11), Vps16, and Vps33, and is necessary for trafficking of hydrolase precursors to the vacuole by promoting vesicular docking reactions with SNARE proteins. Pep3p contains a C3H2C3-type RING-H2 finger at the C-terminus.

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gi 1804891953 816 KCSICNSAL-ELPSVHFLCGHSFHQHCFESYSESD---ADCPTC 855
Cdd:cd16462     2 KCAVCGRPLlTRQFYVFPCQHAFHADCLIEEVLDDliaSECPLC 45

RING finger, H2 subclass, found in RING finger protein 165 (RNF165) and similar proteins; RNF165, also known as Arkadia-like 2, Arkadia2, or Ark2C, is an E3 ubiquitin ligase with homology to the C-terminal half of RNF111. It is expressed specifically in the nervous system, and can serve to amplify neuronal responses to specific signals. It acts as a positive regulator of bone morphogenetic protein (BMP)-Smad signaling that is involved in motor neuron (MN) axon elongation. RNF165 contains two serine rich domains, a nuclear localization signal, an NRG-TIER domain, and a C-terminal C3H2C3-type RING-H2 finger that is responsible for the enhancement of BMP-Smad1/5/8 signaling in the spinal cord.

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gi 1804891953 816 KCSICNSALE-------LPsvhflCGHSFHQHCFESYSESDADCPTC 855
Cdd:cd16682     9 KCTICLSMLEdgedvrrLP-----CMHLFHQLCVDQWLAMSKKCPIC 50