hypothetical protein TGGT1_239410 [Toxoplasma gondii GT1]
Protein Classification
List of domain hits
| Name | Accession | Description | Interval | E-value | |||||||
| MOT2 super family | cl28713 | Transcriptional repressor [Transcription]; |
287-639 | 2.18e-60 | |||||||
Transcriptional repressor [Transcription]; The actual alignment was detected with superfamily member COG5175: Pssm-ID: 227502 [Multi-domain] Cd Length: 480 Bit Score: 216.86 E-value: 2.18e-60
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| PRK07003 super family | cl35530 | DNA polymerase III subunit gamma/tau; |
683-953 | 6.36e-05 | |||||||
DNA polymerase III subunit gamma/tau; The actual alignment was detected with superfamily member PRK07003: Pssm-ID: 235906 [Multi-domain] Cd Length: 830 Bit Score: 48.31 E-value: 6.36e-05
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| PRK07764 super family | cl35613 | DNA polymerase III subunits gamma and tau; Validated |
755-1154 | 7.91e-03 | |||||||
DNA polymerase III subunits gamma and tau; Validated The actual alignment was detected with superfamily member PRK07764: Pssm-ID: 236090 [Multi-domain] Cd Length: 824 Bit Score: 41.51 E-value: 7.91e-03
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| Name | Accession | Description | Interval | E-value | |||||||
| MOT2 | COG5175 | Transcriptional repressor [Transcription]; |
287-639 | 2.18e-60 | |||||||
Transcriptional repressor [Transcription]; Pssm-ID: 227502 [Multi-domain] Cd Length: 480 Bit Score: 216.86 E-value: 2.18e-60
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| RRM_CNOT4 | cd12438 | RNA recognition motif (RRM) found in Eukaryotic CCR4-NOT transcription complex subunit 4 (NOT4) ... |
465-563 | 2.05e-51 | |||||||
RNA recognition motif (RRM) found in Eukaryotic CCR4-NOT transcription complex subunit 4 (NOT4) and similar proteins; This subfamily corresponds to the RRM of NOT4, also termed CCR4-associated factor 4, or E3 ubiquitin-protein ligase CNOT4, or potential transcriptional repressor NOT4Hp, a component of the CCR4-NOT complex, a global negative regulator of RNA polymerase II transcription. NOT4 functions as an ubiquitin-protein ligase (E3). It contains an N-terminal C4C4 type RING finger motif, followed by a RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The RING fingers may interact with a subset of ubiquitin-conjugating enzymes (E2s), including UbcH5B, and mediate protein-protein interactions. T Pssm-ID: 409872 [Multi-domain] Cd Length: 98 Bit Score: 176.57 E-value: 2.05e-51
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| zf-RING_4 | pfam14570 | RING/Ubox like zinc-binding domain; |
287-333 | 9.37e-26 | |||||||
RING/Ubox like zinc-binding domain; Pssm-ID: 405286 [Multi-domain] Cd Length: 47 Bit Score: 101.54 E-value: 9.37e-26
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| RRM | smart00360 | RNA recognition motif; |
472-549 | 1.71e-07 | |||||||
RNA recognition motif; Pssm-ID: 214636 [Multi-domain] Cd Length: 73 Bit Score: 50.28 E-value: 1.71e-07
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| PRK07003 | PRK07003 | DNA polymerase III subunit gamma/tau; |
683-953 | 6.36e-05 | |||||||
DNA polymerase III subunit gamma/tau; Pssm-ID: 235906 [Multi-domain] Cd Length: 830 Bit Score: 48.31 E-value: 6.36e-05
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| PRK07764 | PRK07764 | DNA polymerase III subunits gamma and tau; Validated |
755-1154 | 7.91e-03 | |||||||
DNA polymerase III subunits gamma and tau; Validated Pssm-ID: 236090 [Multi-domain] Cd Length: 824 Bit Score: 41.51 E-value: 7.91e-03
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| Name | Accession | Description | Interval | E-value | |||||||
| MOT2 | COG5175 | Transcriptional repressor [Transcription]; |
287-639 | 2.18e-60 | |||||||
Transcriptional repressor [Transcription]; Pssm-ID: 227502 [Multi-domain] Cd Length: 480 Bit Score: 216.86 E-value: 2.18e-60
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| RRM_CNOT4 | cd12438 | RNA recognition motif (RRM) found in Eukaryotic CCR4-NOT transcription complex subunit 4 (NOT4) ... |
465-563 | 2.05e-51 | |||||||
RNA recognition motif (RRM) found in Eukaryotic CCR4-NOT transcription complex subunit 4 (NOT4) and similar proteins; This subfamily corresponds to the RRM of NOT4, also termed CCR4-associated factor 4, or E3 ubiquitin-protein ligase CNOT4, or potential transcriptional repressor NOT4Hp, a component of the CCR4-NOT complex, a global negative regulator of RNA polymerase II transcription. NOT4 functions as an ubiquitin-protein ligase (E3). It contains an N-terminal C4C4 type RING finger motif, followed by a RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The RING fingers may interact with a subset of ubiquitin-conjugating enzymes (E2s), including UbcH5B, and mediate protein-protein interactions. T Pssm-ID: 409872 [Multi-domain] Cd Length: 98 Bit Score: 176.57 E-value: 2.05e-51
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| mRING-HC-C4C4_CNOT4 | cd16618 | Modified RING finger, HC subclass (C4C4-type), found in CCR4-NOT transcription complex subunit ... |
286-331 | 2.90e-27 | |||||||
Modified RING finger, HC subclass (C4C4-type), found in CCR4-NOT transcription complex subunit 4 (NOT4) and similar proteins; NOT4, also known as CCR4-associated factor 4, E3 ubiquitin-protein ligase CNOT4, or potential transcriptional repressor NOT4, is a component of the multifunctional CCR4-NOT complex, a global regulator of RNA polymerase II transcription. It associates with polysomes and contributes to the negative regulation of protein synthesis. NOT4 functions as an E3 ubiquitin-protein ligase that interacts with a specific E2, Ubc4/5 in yeast, and the ortholog UbcH5B in humans, and ubiquitylates a wide range of substrates, including ribosome-associated factors. Thus, it plays a role in cotranslational quality control (QC) through ribosome-associated ubiquitination and degradation of aberrant peptides. NOT4 contains a C4C4-type RING finger motif, whose overall folding is similar to that of the C3HC4-type RING-HC finger, a central RNA recognition motif (RRM), and a C-terminal domain predicted to be unstructured. Pssm-ID: 438280 [Multi-domain] Cd Length: 47 Bit Score: 105.78 E-value: 2.90e-27
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| zf-RING_4 | pfam14570 | RING/Ubox like zinc-binding domain; |
287-333 | 9.37e-26 | |||||||
RING/Ubox like zinc-binding domain; Pssm-ID: 405286 [Multi-domain] Cd Length: 47 Bit Score: 101.54 E-value: 9.37e-26
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| RRM_SF | cd00590 | RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ... |
472-551 | 1.59e-08 | |||||||
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs). Pssm-ID: 409669 [Multi-domain] Cd Length: 72 Bit Score: 53.44 E-value: 1.59e-08
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| RRM_1 | pfam00076 | RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ... |
472-549 | 4.89e-08 | |||||||
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins have an N terminal rrm which is included in the seed. There is a second region towards the C terminus that has some features characteriztic of a rrm but does not appear to have the important structural core of a rrm. The LA proteins are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease. Pssm-ID: 425453 [Multi-domain] Cd Length: 70 Bit Score: 51.85 E-value: 4.89e-08
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| RRM | smart00360 | RNA recognition motif; |
472-549 | 1.71e-07 | |||||||
RNA recognition motif; Pssm-ID: 214636 [Multi-domain] Cd Length: 73 Bit Score: 50.28 E-value: 1.71e-07
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| RRM1_U1A_like | cd12246 | RNA recognition motif 1 (RRM1) found in the U1A/U2B"/SNF protein family; This subfamily ... |
473-552 | 8.94e-07 | |||||||
RNA recognition motif 1 (RRM1) found in the U1A/U2B"/SNF protein family; This subfamily corresponds to the RRM1 of U1A/U2B"/SNF protein family which contains Drosophila sex determination protein SNF and its two mammalian counterparts, U1 small nuclear ribonucleoprotein A (U1 snRNP A or U1-A or U1A) and U2 small nuclear ribonucleoprotein B" (U2 snRNP B" or U2B"), all of which consist of two RNA recognition motifs (RRMs), connected by a variable, flexible linker. SNF is an RNA-binding protein found in the U1 and U2 snRNPs of Drosophila where it is essential in sex determination and possesses a novel dual RNA binding specificity. SNF binds with high affinity to both Drosophila U1 snRNA stem-loop II (SLII) and U2 snRNA stem-loop IV (SLIV). It can also bind to poly(U) RNA tracts flanking the alternatively spliced Sex-lethal (Sxl) exon, as does Drosophila Sex-lethal protein (SXL). U1A is an RNA-binding protein associated with the U1 snRNP, a small RNA-protein complex involved in pre-mRNA splicing. U1A binds with high affinity and specificity to stem-loop II (SLII) of U1 snRNA. It is predominantly a nuclear protein that shuttles between the nucleus and the cytoplasm independently of interactions with U1 snRNA. Moreover, U1A may be involved in RNA 3'-end processing, specifically cleavage, splicing and polyadenylation, through interacting with a large number of non-snRNP proteins. U2B", initially identified to bind to stem-loop IV (SLIV) at the 3' end of U2 snRNA, is a unique protein that comprises of the U2 snRNP. Additional research indicates U2B" binds to U1 snRNA stem-loop II (SLII) as well and shows no preference for SLIV or SLII on the basis of binding affinity. Moreover, U2B" does not require an auxiliary protein for binding to RNA, and its nuclear transport is independent of U2 snRNA binding. Pssm-ID: 409692 [Multi-domain] Cd Length: 78 Bit Score: 48.68 E-value: 8.94e-07
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| RRM3_PES4_MIP6 | cd21603 | RNA recognition motif 3 (RRM3) found in Saccharomyces cerevisiae protein PES4, protein MIP6 ... |
472-551 | 1.15e-06 | |||||||
RNA recognition motif 3 (RRM3) found in Saccharomyces cerevisiae protein PES4, protein MIP6 and similar proteins; The family includes PES4 (also called DNA polymerase epsilon suppressor 4) and MIP6 (also called MEX67-interacting protein 6), both of which are predicted RNA binding proteins that may act as regulators of late translation, protection, and mRNA localization. MIP6 acts as a novel factor for nuclear mRNA export, binds to both poly(A)+ RNA and nuclear pores. It interacts with MEX67. Members in this family contain four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the third RRM motif. Pssm-ID: 410182 [Multi-domain] Cd Length: 73 Bit Score: 48.05 E-value: 1.15e-06
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| RING-HC_RNF222 | cd16564 | RING finger, HC subclass, found in RING finger protein 222 (RNF222) and similar proteins; ... |
286-332 | 1.67e-06 | |||||||
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: 47.01 E-value: 1.67e-06
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| RRM_1 | smart00361 | RNA recognition motif; |
491-551 | 1.77e-06 | |||||||
RNA recognition motif; Pssm-ID: 214637 [Multi-domain] Cd Length: 70 Bit Score: 47.40 E-value: 1.77e-06
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| zf-RING_2 | pfam13639 | Ring finger domain; |
286-330 | 2.10e-06 | |||||||
Ring finger domain; Pssm-ID: 433370 [Multi-domain] Cd Length: 44 Bit Score: 46.63 E-value: 2.10e-06
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| RING-HC | cd16449 | HC subclass of RING (RING-HC) finger and its variants; The RING finger is a specialized type ... |
286-329 | 4.10e-06 | |||||||
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: 45.55 E-value: 4.10e-06
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| RRM3_U2AF65 | cd12232 | RNA recognition motif 3 (RRM3) found in U2 large nuclear ribonucleoprotein auxiliary factor ... |
484-551 | 8.37e-06 | |||||||
RNA recognition motif 3 (RRM3) found in U2 large nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa subunit (U2AF65) and similar proteins; This subfamily corresponds to the RRM3 of U2AF65 and dU2AF50. U2AF65, also termed U2AF2, is the large subunit of U2 small nuclear ribonucleoprotein (snRNP) auxiliary factor (U2AF), which has been implicated in the recruitment of U2 snRNP to pre-mRNAs and is a highly conserved heterodimer composed of large and small subunits. U2AF65 specifically recognizes the intron polypyrimidine tract upstream of the 3' splice site and promotes binding of U2 snRNP to the pre-mRNA branchpoint. U2AF65 also plays an important role in the nuclear export of mRNA. It facilitates the formation of a messenger ribonucleoprotein export complex, containing both the NXF1 receptor and the RNA substrate. Moreover, U2AF65 interacts directly and specifically with expanded CAG RNA, and serves as an adaptor to link expanded CAG RNA to NXF1 for RNA export. U2AF65 contains an N-terminal RS domain rich in arginine and serine, followed by a proline-rich segment and three C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The N-terminal RS domain stabilizes the interaction of U2 snRNP with the branch point (BP) by contacting the branch region, and further promotes base pair interactions between U2 snRNA and the BP. The proline-rich segment mediates protein-protein interactions with the RRM domain of the small U2AF subunit (U2AF35 or U2AF1). The RRM1 and RRM2 are sufficient for specific RNA binding, while RRM3 is responsible for protein-protein interactions. The family also includes Splicing factor U2AF 50 kDa subunit (dU2AF50), the Drosophila ortholog of U2AF65. dU2AF50 functions as an essential pre-mRNA splicing factor in flies. It associates with intronless mRNAs and plays a significant and unexpected role in the nuclear export of a large number of intronless mRNAs. Pssm-ID: 409679 [Multi-domain] Cd Length: 89 Bit Score: 46.04 E-value: 8.37e-06
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| RING | smart00184 | Ring finger; E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and ... |
287-329 | 2.33e-05 | |||||||
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: 43.27 E-value: 2.33e-05
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| RRM1_PSRP2_like | cd21609 | RNA recognition motif 1 (RRM1) found in chloroplastic plastid-specific 30S ribosomal protein 2 ... |
472-552 | 3.25e-05 | |||||||
RNA recognition motif 1 (RRM1) found in chloroplastic plastid-specific 30S ribosomal protein 2 (PSRP-2) and similar proteins; PSRP-2, also called chloroplastic 30S ribosomal protein 2, or chloroplastic small ribosomal subunit protein cS22, is a component of the chloroplast ribosome (chloro-ribosome), a dedicated translation machinery responsible for the synthesis of chloroplast genome-encoded proteins, including proteins of the transcription and translation machinery and components of the photosynthetic apparatus. It binds single strand DNA (ssDNA) and RNA in vitro. It exhibits RNA chaperone activity and regulates negatively resistance responses to abiotic stresses during seed germination (e.g. salt, dehydration, and low temperature) and seedling growth (e.g. salt). The family also includes Nicotiana sylvestris chloroplastic 33 kDa ribonucleoprotein (NsCP33) and Arabidopsis thaliana chloroplastic 31 kDa ribonucleoprotein (AtCP31A). NsCP33 may be involved in splicing and/or processing of chloroplast RNA's. AtCP31A, also called RNA-binding protein 1/2/3 (AtRBP33), or RNA-binding protein CP31A, or RNA-binding protein RNP-T, or RNA-binding protein cp31, is required for specific RNA editing events in chloroplasts and stabilizes specific chloroplast mRNAs, as well as for normal chloroplast development under cold stress conditions by stabilizing transcripts of numerous mRNAs under these conditions. CP31A may modulate telomere replication through RNA binding domains. Members in this family contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the first RRM motif. Pssm-ID: 410188 [Multi-domain] Cd Length: 80 Bit Score: 44.33 E-value: 3.25e-05
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| RING-HC_PRT1-like | cd23132 | RING finger, HC subclass, found in Arabidopsis thaliana proteolysis 1 protein (PRT1) and ... |
286-334 | 3.39e-05 | |||||||
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: 43.18 E-value: 3.39e-05
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| RING-H2_BRAP2 | cd16457 | RING finger, H2 subclass, found in BRCA1-associated protein (BRAP2) and similar proteins; ... |
286-330 | 3.53e-05 | |||||||
RING finger, H2 subclass, found in BRCA1-associated protein (BRAP2) and similar proteins; BRAP2, also known as impedes mitogenic signal propagation (IMP), RING finger protein 52, or renal carcinoma antigen NY-REN-63, is a novel cytoplasmic protein interacting with the two functional nuclear localization signal (NLS) motifs of BRCA1, a nuclear protein linked to breast cancer. It also binds to the SV40 large T antigen NLS motif and the bipartite NLS motif found in mitosin. BRAP2 serves as a cytoplasmic retention protein and plays a role in the regulation of nuclear protein transport. It contains an N-terminal RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C3H2C3-type RING-H2 finger and a UBP-type zinc finger. Pssm-ID: 438121 [Multi-domain] Cd Length: 44 Bit Score: 43.04 E-value: 3.53e-05
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| RRM3_TIA1_like | cd12354 | RNA recognition motif 2 (RRM2) found in granule-associated RNA binding proteins (p40-TIA-1 and ... |
472-553 | 6.32e-05 | |||||||
RNA recognition motif 2 (RRM2) found in granule-associated RNA binding proteins (p40-TIA-1 and TIAR), and yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1; This subfamily corresponds to the RRM3 of TIA-1, TIAR, and PUB1. Nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and nucleolysin TIA-1-related protein (TIAR) are granule-associated RNA binding proteins involved in inducing apoptosis in cytotoxic lymphocyte (CTL) target cells. They share high sequence similarity and are expressed in a wide variety of cell types. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis.TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. Both TIA-1 and TIAR bind specifically to poly(A) but not to poly(C) homopolymers. They are composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 and TIAR interact with RNAs containing short stretches of uridylates and their RRM2 can mediate the specific binding to uridylate-rich RNAs. The C-terminal auxiliary domain may be responsible for interacting with other proteins. In addition, TIA-1 and TIAR share a potential serine protease-cleavage site (Phe-Val-Arg) localized at the junction between their RNA binding domains and their C-terminal auxiliary domains. This subfamily also includes a yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1, termed ARS consensus-binding protein ACBP-60, or poly uridylate-binding protein, or poly(U)-binding protein, which has been identified as both a heterogeneous nuclear RNA-binding protein (hnRNP) and a cytoplasmic mRNA-binding protein (mRNP). It may be stably bound to a translationally inactive subpopulation of mRNAs within the cytoplasm. PUB1 is distributed in both, the nucleus and the cytoplasm, and binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is one of the major cellular proteins cross-linked by UV light to polyadenylated RNAs in vivo, PUB1 is nonessential for cell growth in yeast. PUB1 also binds to T-rich single stranded DNA (ssDNA); however, there is no strong evidence implicating PUB1 in the mechanism of DNA replication. PUB1 contains three RRMs, and a GAR motif (glycine and arginine rich stretch) that is located between RRM2 and RRM3. Pssm-ID: 409790 [Multi-domain] Cd Length: 71 Bit Score: 43.04 E-value: 6.32e-05
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| PRK07003 | PRK07003 | DNA polymerase III subunit gamma/tau; |
683-953 | 6.36e-05 | |||||||
DNA polymerase III subunit gamma/tau; Pssm-ID: 235906 [Multi-domain] Cd Length: 830 Bit Score: 48.31 E-value: 6.36e-05
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| RING-HC_TRIM21_C-IV | cd16596 | RING finger, HC subclass, found in tripartite motif-containing protein TRIM21 and similar ... |
286-343 | 6.71e-05 | |||||||
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: 43.35 E-value: 6.71e-05
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| RRM_ZCRB1 | cd12393 | RNA recognition motif (RRM) found in Zinc finger CCHC-type and RNA-binding motif-containing ... |
469-551 | 8.59e-05 | |||||||
RNA recognition motif (RRM) found in Zinc finger CCHC-type and RNA-binding motif-containing protein 1 (ZCRB1) and similar proteins; This subfamily corresponds to the RRM of ZCRB1, also termed MADP-1, or U11/U12 small nuclear ribonucleoprotein 31 kDa protein (U11/U12 snRNP 31 or U11/U12-31K), a novel multi-functional nuclear factor, which may be involved in morphine dependence, cold/heat stress, and hepatocarcinoma. It is located in the nucleoplasm, but outside the nucleolus. ZCRB1 is one of the components of U11/U12 snRNPs that bind to U12-type pre-mRNAs and form a di-snRNP complex, simultaneously recognizing the 5' splice site and branchpoint sequence. ZCRB1 is characterized by an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a CCHC-type Zinc finger motif. In addition, it contains core nucleocapsid motifs, and Lys- and Glu-rich domains. Pssm-ID: 409827 [Multi-domain] Cd Length: 76 Bit Score: 43.04 E-value: 8.59e-05
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| PRK12678 | PRK12678 | transcription termination factor Rho; Provisional |
784-972 | 1.03e-04 | |||||||
transcription termination factor Rho; Provisional Pssm-ID: 237171 [Multi-domain] Cd Length: 672 Bit Score: 47.59 E-value: 1.03e-04
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| PRK07003 | PRK07003 | DNA polymerase III subunit gamma/tau; |
784-975 | 1.51e-04 | |||||||
DNA polymerase III subunit gamma/tau; Pssm-ID: 235906 [Multi-domain] Cd Length: 830 Bit Score: 47.15 E-value: 1.51e-04
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| RRM | COG0724 | RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]; |
473-549 | 1.69e-04 | |||||||
RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]; Pssm-ID: 440488 [Multi-domain] Cd Length: 85 Bit Score: 42.39 E-value: 1.69e-04
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| RRM_UHM_SPF45_PUF60 | cd12374 | RNA recognition motif (RRM) found in UHM domain of 45 kDa-splicing factor (SPF45) and similar ... |
483-552 | 2.20e-04 | |||||||
RNA recognition motif (RRM) found in UHM domain of 45 kDa-splicing factor (SPF45) and similar proteins; This subfamily corresponds to the RRM found in UHM domain of 45 kDa-splicing factor (SPF45 or RBM17), poly(U)-binding-splicing factor PUF60 (FIR or Hfp or RoBP1 or Siah-BP1), and similar proteins. SPF45 is an RNA-binding protein consisting of an unstructured N-terminal region, followed by a G-patch motif and a C-terminal U2AF (U2 auxiliary factor) homology motifs (UHM) that harbors a RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain) and an Arg-Xaa-Phe sequence motif. SPF45 regulates alternative splicing of the apoptosis regulatory gene FAS (also known as CD95). It induces exon 6 skipping in FAS pre-mRNA through the UHM domain that binds to tryptophan-containing linear peptide motifs (UHM ligand motifs, ULMs) present in the 3' splice site-recognizing factors U2AF65, SF1 and SF3b155. PUF60 is an essential splicing factor that functions as a poly-U RNA-binding protein required to reconstitute splicing in depleted nuclear extracts. Its function is enhanced through interaction with U2 auxiliary factor U2AF65. PUF60 also controls human c-myc gene expression by binding and inhibiting the transcription factor far upstream sequence element (FUSE)-binding-protein (FBP), an activator of c-myc promoters. PUF60 contains two central RRMs and a C-terminal UHM domain. Pssm-ID: 409809 [Multi-domain] Cd Length: 85 Bit Score: 42.21 E-value: 2.20e-04
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| PRK12678 | PRK12678 | transcription termination factor Rho; Provisional |
738-929 | 3.04e-04 | |||||||
transcription termination factor Rho; Provisional Pssm-ID: 237171 [Multi-domain] Cd Length: 672 Bit Score: 46.05 E-value: 3.04e-04
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| RRM_SAFB_like | cd12417 | RNA recognition motif (RRM) found in the scaffold attachment factor (SAFB) family; This ... |
473-548 | 4.07e-04 | |||||||
RNA recognition motif (RRM) found in the scaffold attachment factor (SAFB) family; This subfamily corresponds to the RRM domain of the SAFB family, including scaffold attachment factor B1 (SAFB1), scaffold attachment factor B2 (SAFB2), SAFB-like transcriptional modulator (SLTM), and similar proteins, which are ubiquitously expressed. SAFB1, SAFB2 and SLTM have been implicated in many diverse cellular processes including cell growth and transformation, stress response, and apoptosis. They share high sequence similarities and all contain a scaffold attachment factor-box (SAF-box, also known as SAP domain) DNA-binding motif, an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region rich in glutamine and arginine residues. SAFB1 is a nuclear protein with a distribution similar to that of SLTM, but unlike that of SAFB2, which is also found in the cytoplasm. To a large extent, SAFB1 and SLTM might share similar functions, such as the inhibition of an oestrogen reporter gene. The additional cytoplasmic localization of SAFB2 implies that it could play additional roles in the cytoplasmic compartment which are distinct from the nuclear functions shared with SAFB1 and SLTM. Pssm-ID: 409851 [Multi-domain] Cd Length: 74 Bit Score: 41.09 E-value: 4.07e-04
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| RRM3_HRB1_GBP2 | cd21607 | RNA recognition motif 3 (RRM3) found in Saccharomyces cerevisiae protein HRB1, ... |
470-552 | 6.99e-04 | |||||||
RNA recognition motif 3 (RRM3) found in Saccharomyces cerevisiae protein HRB1, G-strand-binding protein 2 (GBP2) and similar proteins; The family includes Saccharomyces cerevisiae protein HRB1 (also called protein TOM34) and GBP2, both of which are SR-like mRNA-binding proteins which shuttle from the nucleus to the cytoplasm when bound to the mature mRNA molecules. They act as quality control factors for spliced mRNAs. GBP2, also called RAP1 localization factor 6, is a single-strand telomeric DNA-binding protein that binds single-stranded telomeric sequences of the type (TG[1-3])n in vitro. It also binds to RNA. GBP2 influences the localization of RAP1 in the nuclei and plays a role in modulating telomere length. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the third RRM motif. Pssm-ID: 410186 [Multi-domain] Cd Length: 79 Bit Score: 40.39 E-value: 6.99e-04
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| RRM3_RBM39_like | cd12285 | RNA recognition motif 3 (RRM3) found in vertebrate RNA-binding protein 39 (RBM39) and similar ... |
496-552 | 7.33e-04 | |||||||
RNA recognition motif 3 (RRM3) found in vertebrate RNA-binding protein 39 (RBM39) and similar proteins; This subfamily corresponds to the RRM3 of RBM39, also termed hepatocellular carcinoma protein 1, or RNA-binding region-containing protein 2, or splicing factor HCC1, ia nuclear autoantigen that contains an N-terminal arginine/serine rich (RS) motif and three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). An octapeptide sequence called the RS-ERK motif is repeated six times in the RS region of RBM39. Based on the specific domain composition, RBM39 has been classified into a family of non-snRNP (small nuclear ribonucleoprotein) splicing factors that are usually not complexed to snRNAs. Pssm-ID: 409727 [Multi-domain] Cd Length: 85 Bit Score: 40.61 E-value: 7.33e-04
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| zf-C3HC4 | pfam00097 | Zinc finger, C3HC4 type (RING finger); The C3HC4 type zinc-finger (RING finger) is a ... |
287-329 | 7.40e-04 | |||||||
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: 39.26 E-value: 7.40e-04
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| RING-HC_TRIM32_C-VII | cd16587 | RING finger, HC subclass, found in tripartite motif-containing protein 32 (TRIM32) and similar ... |
286-331 | 1.52e-03 | |||||||
RING finger, HC subclass, found in tripartite motif-containing protein 32 (TRIM32) and similar proteins; TRIM32, also known as 72 kDa Tat-interacting protein, zinc finger protein HT2A, or BBS11, is an E3 ubiquitin-protein ligase that promotes degradation of several targets, including actin, PIASgamma, Abl interactor 2, dysbindin, X-linked inhibitor of apoptosis (XIAP), p73 transcription factor, thin filaments and Z-bands during fasting. It plays important roles in neuronal differentiation of neural progenitor cells, as well as in controlling cell fate in skeletal muscle progenitor cells. It reduces PI3K-Akt-FoxO signaling in muscle atrophy by promoting plakoglobin-PI3K dissociation. It also functions as a pluripotency-reprogramming roadblock that facilitates cellular transition towards differentiation by modulating the levels of Oct4 and cMyc. Moreover, TRIM32 is an intrinsic influenza A virus (IAV) restriction factor which senses and targets the polymerase basic protein 1 (PB1) for ubiquitination and protein degradation. It also plays a significant role in mediating the biological activity of the HIV-1 Tat protein in vivo, binds specifically to the activation domain of HIV-1 Tat, and can also interact with the HIV-2 and EIAV Tat proteins in vivo. Furthermore, TRIM32 regulates myoblast proliferation by controlling turnover of NDRG2 (N-myc downstream-regulated gene). It negatively regulates tumor suppressor p53 to promote tumorigenesis. It also facilitates degradation of MYCN on spindle poles and induces asymmetric cell division in human neuroblastoma cells. In addition, TRIM32 plays important roles in regulation of hyperactivities and positively regulates the development of anxiety and depression disorders induced by chronic stress. It also plays a role in regeneration by affecting satellite cell cycle progression via modulation of the SUMO ligase PIASy (PIAS4). Defects in TRIM32 leads to limb-girdle muscular dystrophy type 2H (LGMD2H), sarcotubular myopathies (STM) and Bardet-Biedl syndrome. TRIM32 belongs to the C-VII subclass of the TRIM (tripartite motif)-NHL family that is defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil domain, as well as a NHL (named after proteins NCL-1, HT2A and Lin-41 that contain repeats folded into a six-bladed beta propeller) repeat domain positioned C-terminal to the RBCC domain. The NHL domain mediates the interaction with Argonaute proteins and consequently allows TRIM32 to modulate the activity of certain miRNAs. Pssm-ID: 438249 [Multi-domain] Cd Length: 51 Bit Score: 38.54 E-value: 1.52e-03
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| RRM_NOL8 | cd12226 | RNA recognition motif (RRM) found in nucleolar protein 8 (NOL8) and similar proteins; This ... |
472-549 | 1.64e-03 | |||||||
RNA recognition motif (RRM) found in nucleolar protein 8 (NOL8) and similar proteins; This model corresponds to the RRM of NOL8 (also termed Nop132) encoded by a novel NOL8 gene that is up-regulated in the majority of diffuse-type, but not intestinal-type, gastric cancers. Thus, NOL8 may be a good molecular target for treatment of diffuse-type gastric cancer. Also, NOL8 is a phosphorylated protein that contains an N-terminal RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), suggesting NOL8 is likely to function as a novel RNA-binding protein. It may be involved in regulation of gene expression at the post-transcriptional level or in ribosome biogenesis in cancer cells. Pssm-ID: 409673 [Multi-domain] Cd Length: 77 Bit Score: 39.48 E-value: 1.64e-03
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| RING-H2_ASR1 | cd23120 | RING finger, H2 subclass, found in Saccharomyces cerevisiae alcohol-sensitive RING finger ... |
287-332 | 1.76e-03 | |||||||
RING finger, H2 subclass, found in Saccharomyces cerevisiae alcohol-sensitive RING finger protein 1 (ASR1) and similar proteins; ASR1 is required for tolerance to alcohol. It signals alcohol stress to the nucleus. ASR1 contains a C3H2C3-type RING-H2 finger. Pssm-ID: 438482 [Multi-domain] Cd Length: 54 Bit Score: 38.67 E-value: 1.76e-03
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| RING-HC_SH3RFs | cd16570 | RING finger, HC subclass, found in SH3 domain-containing RING finger proteins SH3RF1, SH3RF2, ... |
287-330 | 1.97e-03 | |||||||
RING finger, HC subclass, found in SH3 domain-containing RING finger proteins SH3RF1, SH3RF2, SH3RF3, and similar proteins; SH3RF1, also known as plenty of SH3s (POSH), RING finger protein 142 (RNF142), or SH3 multiple domains protein 2 (SH3MD2), is a trans-Golgi network-associated pro-apoptotic scaffold protein with E3 ubiquitin-protein ligase activity. SH3RF2, also known as heart protein phosphatase 1-binding protein (HEPP1), plenty of SH3s (POSH)-eliminating RING protein (POSHER), protein phosphatase 1 regulatory subunit 39, or RING finger protein 158 (RNF158), is a putative E3 ubiquitin-protein ligase that acts as an anti-apoptotic regulator for the c-Jun N-terminal kinase (JNK) pathway by binding to and promoting the proteasomal degradation of SH3RF1 (or POSH) that is required for pro-apoptotic JNK activation. SH3RF3, also known as plenty of SH3s 2 (POSH2) or SH3 multiple domains protein 4 (SH3MD4), is a scaffold protein with E3 ubiquitin-protein ligase activity. It was identified in the screen for interacting partners of p21-activated kinase 2 (PAK2) and may play a role in regulating c-Jun N-terminal kinase (JNK) mediated apoptosis in certain conditions. Members of this subfamily contain an N-terminal C3HC4-type RING-HC finger responsible for the E3 ligase activity and four Src Homology 3 (SH3) domains, which are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Pssm-ID: 438232 [Multi-domain] Cd Length: 44 Bit Score: 38.18 E-value: 1.97e-03
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| RRM3_RBM19_RRM2_MRD1 | cd12316 | RNA recognition motif 3 (RRM3) found in RNA-binding protein 19 (RBM19) and RNA recognition ... |
491-548 | 2.11e-03 | |||||||
RNA recognition motif 3 (RRM3) found in RNA-binding protein 19 (RBM19) and RNA recognition motif 2 found in multiple RNA-binding domain-containing protein 1 (MRD1); This subfamily corresponds to the RRM3 of RBM19 and RRM2 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events. Pssm-ID: 409755 [Multi-domain] Cd Length: 74 Bit Score: 38.86 E-value: 2.11e-03
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| RING-HC_SH3RF2 | cd16749 | RING finger, HC subclass, found in SH3 domain-containing RING finger protein 2 (SH3RF2) and ... |
287-330 | 3.01e-03 | |||||||
RING finger, HC subclass, found in SH3 domain-containing RING finger protein 2 (SH3RF2) and similar proteins; SH3RF2, also known as heart protein phosphatase 1-binding protein (HEPP1), plenty of SH3s (POSH)-eliminating RING protein (POSHER), protein phosphatase 1 regulatory subunit 39, or RING finger protein 158 (RNF158), is a putative E3 ubiquitin-protein ligase that acts as an anti-apoptotic regulator for the c-Jun N-terminal kinase (JNK) pathway by binding to and promoting the proteasomal degradation of SH3RF1 (or POSH), a scaffold protein that is required for pro-apoptotic JNK activation. It may also play a role in cardiac functions together with protein phosphatase 1. SH3RF2 contains an N-terminal C3HC4-type RING-HC finger responsible for the E3 ligase activity and four Src Homology 3 (SH3) domains, which are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Pssm-ID: 438407 [Multi-domain] Cd Length: 46 Bit Score: 37.61 E-value: 3.01e-03
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| PRK07764 | PRK07764 | DNA polymerase III subunits gamma and tau; Validated |
702-1134 | 3.02e-03 | |||||||
DNA polymerase III subunits gamma and tau; Validated Pssm-ID: 236090 [Multi-domain] Cd Length: 824 Bit Score: 43.05 E-value: 3.02e-03
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| RRM3_Hu | cd12377 | RNA recognition motif 3 (RRM3) found in the Hu proteins family; This subfamily corresponds to ... |
493-552 | 3.18e-03 | |||||||
RNA recognition motif 3 (RRM3) found in the Hu proteins family; This subfamily corresponds to the RRM3 of the Hu proteins family which represent a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. Pssm-ID: 409811 [Multi-domain] Cd Length: 76 Bit Score: 38.46 E-value: 3.18e-03
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| PRK07764 | PRK07764 | DNA polymerase III subunits gamma and tau; Validated |
634-830 | 3.89e-03 | |||||||
DNA polymerase III subunits gamma and tau; Validated Pssm-ID: 236090 [Multi-domain] Cd Length: 824 Bit Score: 42.67 E-value: 3.89e-03
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| RING-HC_COP1 | cd16504 | RING finger, HC subclass, found in constitutive photomorphogenesis protein 1 (COP1) and ... |
286-334 | 4.23e-03 | |||||||
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: 37.22 E-value: 4.23e-03
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| PHA03307 | PHA03307 | transcriptional regulator ICP4; Provisional |
755-1128 | 5.38e-03 | |||||||
transcriptional regulator ICP4; Provisional Pssm-ID: 223039 [Multi-domain] Cd Length: 1352 Bit Score: 42.47 E-value: 5.38e-03
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| RING-H2_Rapsyn | cd16478 | RING finger, H2 subclass, found in 43 kDa receptor-associated protein of the synapse (Rapsyn) ... |
287-331 | 5.48e-03 | |||||||
RING finger, H2 subclass, found in 43 kDa receptor-associated protein of the synapse (Rapsyn) and similar proteins; Rapsyn, also known as acetylcholine receptor (AChR)-associated 43 kDa protein or RING finger protein 205 (RNF205), is a 43 kDa postsynaptic protein that plays an essential role in the clustering and maintenance of AChR in the postsynaptic membrane of the motor endplate. AChRs enable the transport of rapsyn from the Golgi complex to the plasma membrane through a molecule-specific interaction. Rapsyn also mediates subsynaptic anchoring of protein kinase A (PKA) type I in close proximity to the postsynaptic membrane, which is essential for synapse maintenance. Its mutations in humans cause endplate AChR deficiency and myasthenic syndrome. Rapsyn contains an N-terminal myristoylation signal required for membrane association, seven tetratricopeptide repeats (TPRs) that subserve rapsyn self-association, a coiled-coil domain responsible for the binding of determinants within the long cytoplasmic loop of each AChR subunit, a C3H2C3-type RING-H2 finger that binds to the cytoplasmic domain of beta-dystroglycan and to S-NRAP and links rapsyn to the subsynaptic cytoskeleton, and a serine phosphorylation site. Pssm-ID: 438141 [Multi-domain] Cd Length: 48 Bit Score: 37.05 E-value: 5.48e-03
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| RING-CH-C4HC3_ZSWM2 | cd16494 | RING-CH finger, H2 subclass (C4HC3-type), found in zinc finger SWIM domain-containing protein ... |
286-333 | 7.03e-03 | |||||||
RING-CH finger, H2 subclass (C4HC3-type), found in zinc finger SWIM domain-containing protein 2 (ZSWIM2) and similar proteins; ZSWIM2, also known as MEKK1-related protein X (MEX) or ZZ-type zinc finger-containing protein 2, is a testis-specific E3 ubiquitin ligase that promotes death receptor-induced apoptosis through Fas, death receptor (DR) 3, and DR4 signaling. ZSWIM2 is self-ubiquitinated and targeted for degradation through the proteasome pathway. It also acts as an E3 ubiquitin ligase, through the E2, Ub-conjugating enzymes UbcH5a, UbcH5c, or UbcH6. ZSWIM2 contains four putative zinc-binding domains including an N-terminal SWIM (SWI2/SNF2 and MuDR) domain critical for its ubiquitination and two RING fingers separated by a ZZ zinc finger domain, which was required for interaction with UbcH5a and its self-association. This model corresponds to the first RING finger, which is a C4HC3-type RING-CH finger, also known as vRING or RINGv, rather than the canonical C3H2C3-type RING-H2 finger. Pssm-ID: 438157 [Multi-domain] Cd Length: 57 Bit Score: 36.93 E-value: 7.03e-03
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| PRK07764 | PRK07764 | DNA polymerase III subunits gamma and tau; Validated |
755-1154 | 7.91e-03 | |||||||
DNA polymerase III subunits gamma and tau; Validated Pssm-ID: 236090 [Multi-domain] Cd Length: 824 Bit Score: 41.51 E-value: 7.91e-03
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| PRK07764 | PRK07764 | DNA polymerase III subunits gamma and tau; Validated |
757-1182 | 8.39e-03 | |||||||
DNA polymerase III subunits gamma and tau; Validated Pssm-ID: 236090 [Multi-domain] Cd Length: 824 Bit Score: 41.51 E-value: 8.39e-03
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| RING-H2_AIRP1-like | cd23116 | RING finger, H2 subclass, found in Arabidopsis thaliana protein ABA INSENSITIVE RING PROTEIN 1 ... |
287-332 | 8.87e-03 | |||||||
RING finger, H2 subclass, found in Arabidopsis thaliana protein ABA INSENSITIVE RING PROTEIN 1 (AIRP1) and similar proteins; This subfamily includes Arabidopsis thaliana AIRP1 and RING-H2 finger B1a (RHB1A). AIRP1, also known as RING-type E3 ubiquitin transferase AIRP1, possesses E3 ubiquitin-protein ligase activity in vitro when associated with the E2 enzyme UBC8. It plays combinatory roles with AIRP2 in the positive regulation of the abscisic acid-mediated drought stress response. RHB1A is a probable E3 ubiquitin-protein ligase. Members of this subfamily contain a C3H2C3-type RING-H2 finger. Pssm-ID: 438478 [Multi-domain] Cd Length: 49 Bit Score: 36.29 E-value: 8.87e-03
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