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 42563493    20 AQQLPASLRAALTYSLGVFALRRSFLhkilDYEDEFFAALMLILEGHSLRTTDGSFAESLYGLRRKSARLRLRKDSarkd 99
Cdd:pfam04757   1 DEELESLLRPQLRYILRLLAGQRFPL----NYFDEIKLLLDLLYFRLTLLRGNATLGEEYYGLKRVSDRDGGRLLS---- 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563493   100 sseevqhsgleKRQRILSVVFLVVLPYFKSKLHAIYNKEREARLRESLWgaedqgfdeadfftgddsivsrepsgneels 179
Cdd:pfam04757  73 -----------RRRRLLSLLLLVLLPYLLRKLDSLLPRLSANDLESRNA------------------------------- 110

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563493   180 vRVQLATKIKKFIAVCYPWIHASSEGLSFTYQLLYLLdaTGFYSLGLQALGIQVCRATGQELMDTSSRISkirnhererl 259
Cdd:pfam04757 111 -RDSLKSRLKRYLLKLYPFLESLYKLLNLHLFLFYLT--GKYYSLSKRLLGIRYVRLKPLDIFSNERRVS---------- 177

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....
gi 42563493   260 rgppwlktVQGALLSCSYAVLDYAQTGLIAAVFIFKMMEWWYQS 303
Cdd:pfam04757 178 --------YEQLLWNAFSELLGFLLPLLLAVILFLKLLEWWYSS 213

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 42563493    20 AQQLPASLRAALTYSLGVFALRRSFLhkilDYEDEFFAALMLILEGHSLRTTDGSFAESLYGLRRKSARLRLRKDSarkd 99
Cdd:pfam04757   1 DEELESLLRPQLRYILRLLAGQRFPL----NYFDEIKLLLDLLYFRLTLLRGNATLGEEYYGLKRVSDRDGGRLLS---- 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563493   100 sseevqhsgleKRQRILSVVFLVVLPYFKSKLHAIYNKEREARLRESLWgaedqgfdeadfftgddsivsrepsgneels 179
Cdd:pfam04757  73 -----------RRRRLLSLLLLVLLPYLLRKLDSLLPRLSANDLESRNA------------------------------- 110

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563493   180 vRVQLATKIKKFIAVCYPWIHASSEGLSFTYQLLYLLdaTGFYSLGLQALGIQVCRATGQELMDTSSRISkirnhererl 259
Cdd:pfam04757 111 -RDSLKSRLKRYLLKLYPFLESLYKLLNLHLFLFYLT--GKYYSLSKRLLGIRYVRLKPLDIFSNERRVS---------- 177

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....
gi 42563493   260 rgppwlktVQGALLSCSYAVLDYAQTGLIAAVFIFKMMEWWYQS 303
Cdd:pfam04757 178 --------YEQLLWNAFSELLGFLLPLLLAVILFLKLLEWWYSS 213

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)

                           10        20        30
                   ....*....|....*....|....*....|....*....
gi 42563493    339 CALCLQKRANPSVVTVSGFVFCYSCVFKYV-SKYKRCPV 376
Cdd:smart00184   1 CPICLEEYLKDPVILPCGHTFCRSCIRKWLeSGNNTCPI 39

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 42563493    20 AQQLPASLRAALTYSLGVFALRRSFLhkilDYEDEFFAALMLILEGHSLRTTDGSFAESLYGLRRKSARLRLRKDSarkd 99
Cdd:pfam04757   1 DEELESLLRPQLRYILRLLAGQRFPL----NYFDEIKLLLDLLYFRLTLLRGNATLGEEYYGLKRVSDRDGGRLLS---- 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563493   100 sseevqhsgleKRQRILSVVFLVVLPYFKSKLHAIYNKEREARLRESLWgaedqgfdeadfftgddsivsrepsgneels 179
Cdd:pfam04757  73 -----------RRRRLLSLLLLVLLPYLLRKLDSLLPRLSANDLESRNA------------------------------- 110

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42563493   180 vRVQLATKIKKFIAVCYPWIHASSEGLSFTYQLLYLLdaTGFYSLGLQALGIQVCRATGQELMDTSSRISkirnhererl 259
Cdd:pfam04757 111 -RDSLKSRLKRYLLKLYPFLESLYKLLNLHLFLFYLT--GKYYSLSKRLLGIRYVRLKPLDIFSNERRVS---------- 177

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....
gi 42563493   260 rgppwlktVQGALLSCSYAVLDYAQTGLIAAVFIFKMMEWWYQS 303
Cdd:pfam04757 178 --------YEQLLWNAFSELLGFLLPLLLAVILFLKLLEWWYSS 213

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.

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|.
gi 42563493 339 CALCLQKRANPSVvTVSGFVFCYSCVFKYVSKYKRCPVTLIPASVDQIRRL 389
Cdd:cd16527   3 CSLCLEERRHPTA-TPCGHLFCWSCITEWCNEKPECPLCREPFQPQRLVPL 52

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.

                        10        20        30
                ....*....|....*....|....*....|....*....
gi 42563493 338 LCALCLQKRANPsVVTVSGFVFCYSCVFKYVSKYKRCPV 376
Cdd:cd16637   3 TCHICLQPLVEP-LDTPCGHTFCYKCLTNYLKIQQCCPL 40

U-box domain, a modified RING finger, found in peptidyl-prolyl cis-trans isomerase-like 2 (PPIL2) and similar proteins; PPIL2 (EC 5.2.1.8), also known as PPIase, CYC4, cyclophilin-60 (Cyp60), cyclophilin-like protein Cyp-60, or Rotamase PPIL2, is a nuclear-specific cyclophilin which interacts with the proteinase inhibitor eglin c and regulates gene expression. PPIL2 belongs to the cyclophilin family of peptidylprolyl isomerases and catalyzes cis-trans isomerization of proline-peptide bonds, which is often a rate-limiting step in protein folding. It positively regulates beta-site amyloid precursor protein cleaving enzyme (BACE1) expression and beta-secretase activity. Moreover, PPIL2 plays an important role in the translocation of CD147 to the cell surface, and thus may present a novel target for therapeutic interventions in diseases where CD147 functions as a pathogenic factor in cancer, human immunodeficiency virus infection, or rheumatoid arthritis. PPIL2 contains an N-terminal RING-like U-box domain and a C-terminal cyclophilin (Cyp)-like chaperone domain.

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|.
gi 42563493 339 CALCLQKRANPsVVTVSGFVFCYSCVFKYVSKYKRCPVTLIPASVDQIRRL 389
Cdd:cd16663   5 CALSLQPFENP-VCTPDGIVFDLLNIVPYLKKYGKNPVTGEPLEAKDLIKL 54

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.

                        10        20        30
                ....*....|....*....|....*....|....*....
gi 42563493 339 CALCLQKRANPsVVTVSGFVFCYSCVFKYV-SKYKRCPV 376
Cdd:cd16449   3 CPICLERLKDP-VLLPCGHVFCRECIRRLLeSGSIKCPI 40

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.

                        10        20        30        40
                ....*....|....*....|....*....|....*....|.
gi 42563493 339 CALCLQKRANPsVVTVSGFVFCYSCVFKYV---SKYKRCPV 376
Cdd:cd16745   3 CNICLDLAQDP-VVTLCGHLFCWPCLHKWLrrqSSQPECPV 42

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
                ....*....|....*....|....*....|....*.
gi 42563493 339 CALCLQKRANPsVVTVSGFVFCYSCVFKYVSKYKRC 374
Cdd:cd23142   3 CPICNDPPEDA-VVTLCGHVFCCECVFQYLSSDRTC 37