RecName: Full=Polyribonucleotide nucleotidyltransferase 2, mitochondrial; AltName: Full=Polynucleotide phosphorylase 2; Short=PNPase 2; Flags: Precursor
Protein Classification
List of domain hits
| Name | Accession | Description | Interval | E-value | ||||||||||
| Pnp | COG1185 | Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ... |
62-758 | 0e+00 | ||||||||||
Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]; : Pssm-ID: 440798 [Multi-domain] Cd Length: 686 Bit Score: 880.88 E-value: 0e+00
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| S1 | smart00316 | Ribosomal protein S1-like RNA-binding domain; |
918-980 | 8.55e-06 | ||||||||||
Ribosomal protein S1-like RNA-binding domain; : Pssm-ID: 197648 [Multi-domain] Cd Length: 72 Bit Score: 44.52 E-value: 8.55e-06
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| Name | Accession | Description | Interval | E-value | ||||||||||
| Pnp | COG1185 | Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ... |
62-758 | 0e+00 | ||||||||||
Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]; Pssm-ID: 440798 [Multi-domain] Cd Length: 686 Bit Score: 880.88 E-value: 0e+00
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| PRK11824 | PRK11824 | polynucleotide phosphorylase/polyadenylase; Provisional |
59-760 | 0e+00 | ||||||||||
polynucleotide phosphorylase/polyadenylase; Provisional Pssm-ID: 236995 [Multi-domain] Cd Length: 693 Bit Score: 855.50 E-value: 0e+00
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| polynuc_phos | TIGR03591 | polyribonucleotide nucleotidyltransferase; Members of this protein family are ... |
66-759 | 0e+00 | ||||||||||
polyribonucleotide nucleotidyltransferase; Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family). [Transcription, Degradation of RNA] Pssm-ID: 274664 [Multi-domain] Cd Length: 688 Bit Score: 801.34 E-value: 0e+00
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| RNase_PH_PNPase_2 | cd11364 | Polyribonucleotide nucleotidyltransferase, repeat 2; Polyribonucleotide nucleotidyltransferase ... |
387-614 | 3.33e-138 | ||||||||||
Polyribonucleotide nucleotidyltransferase, repeat 2; Polyribonucleotide nucleotidyltransferase (PNPase) is a member of the RNase_PH family, named after the bacterial Ribonuclease PH, a 3'-5' exoribonuclease. Structurally, all members of this family form hexameric rings. In the case of PNPase the complex is a trimer, since each monomer contains two tandem copies of the domain. PNPase is involved in mRNA degradation in a 3'-5' direction and in quality control of ribosomal RNA precursors, with the second repeat containing the active site. PNPase is part of the RNA degradosome complex and binds to the scaffolding domain of the endoribonuclease RNase E. Pssm-ID: 206769 [Multi-domain] Cd Length: 223 Bit Score: 412.71 E-value: 3.33e-138
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| RNase_PH | pfam01138 | 3' exoribonuclease family, domain 1; This family includes 3'-5' exoribonucleases. Ribonuclease ... |
387-520 | 2.40e-34 | ||||||||||
3' exoribonuclease family, domain 1; This family includes 3'-5' exoribonucleases. Ribonuclease PH contains a single copy of this domain, and removes nucleotide residues following the -CCA terminus of tRNA. Polyribonucleotide nucleotidyltransferase (PNPase) contains two tandem copies of the domain. PNPase is involved in mRNA degradation in a 3'-5' direction. The exosome is a 3'-5' exoribonuclease complex that is required for 3' processing of the 5.8S rRNA. Three of its five protein components contain a copy of this domain. A hypothetical protein from S. pombe appears to belong to an uncharacterized subfamily. This subfamily is found in both eukaryotes and archaebacteria. Pssm-ID: 426074 [Multi-domain] Cd Length: 129 Bit Score: 127.71 E-value: 2.40e-34
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| S1 | smart00316 | Ribosomal protein S1-like RNA-binding domain; |
687-757 | 1.12e-11 | ||||||||||
Ribosomal protein S1-like RNA-binding domain; Pssm-ID: 197648 [Multi-domain] Cd Length: 72 Bit Score: 61.08 E-value: 1.12e-11
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| S1_dom_CvfD | NF040579 | CvfD/Ygs/GSP13 family RNA-binding post-transcriptional regulator; CvfD, Ygs, and GSP13 form a ... |
686-767 | 5.84e-11 | ||||||||||
CvfD/Ygs/GSP13 family RNA-binding post-transcriptional regulator; CvfD, Ygs, and GSP13 form a family of full-length homologs of RNA-binding proteins from the Firmicutes with a single copy of the S1 domain. Several members of the family have been characterized as general stress proteins, and the most recently characterized, CvfD, was shown to act as a post-transcriptional regulator. Pssm-ID: 468553 [Multi-domain] Cd Length: 113 Bit Score: 60.52 E-value: 5.84e-11
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| S1 | smart00316 | Ribosomal protein S1-like RNA-binding domain; |
918-980 | 8.55e-06 | ||||||||||
Ribosomal protein S1-like RNA-binding domain; Pssm-ID: 197648 [Multi-domain] Cd Length: 72 Bit Score: 44.52 E-value: 8.55e-06
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| PRK08059 | PRK08059 | general stress protein 13; Validated |
913-966 | 4.76e-03 | ||||||||||
general stress protein 13; Validated Pssm-ID: 181215 [Multi-domain] Cd Length: 123 Bit Score: 38.10 E-value: 4.76e-03
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| Name | Accession | Description | Interval | E-value | ||||||||||||
| Pnp | COG1185 | Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ... |
62-758 | 0e+00 | ||||||||||||
Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]; Pssm-ID: 440798 [Multi-domain] Cd Length: 686 Bit Score: 880.88 E-value: 0e+00
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| PRK11824 | PRK11824 | polynucleotide phosphorylase/polyadenylase; Provisional |
59-760 | 0e+00 | ||||||||||||
polynucleotide phosphorylase/polyadenylase; Provisional Pssm-ID: 236995 [Multi-domain] Cd Length: 693 Bit Score: 855.50 E-value: 0e+00
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| polynuc_phos | TIGR03591 | polyribonucleotide nucleotidyltransferase; Members of this protein family are ... |
66-759 | 0e+00 | ||||||||||||
polyribonucleotide nucleotidyltransferase; Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family). [Transcription, Degradation of RNA] Pssm-ID: 274664 [Multi-domain] Cd Length: 688 Bit Score: 801.34 E-value: 0e+00
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| pppGpp_PNP | TIGR02696 | guanosine pentaphosphate synthetase I/polynucleotide phosphorylase; Sohlberg, et al. present ... |
68-721 | 1.71e-165 | ||||||||||||
guanosine pentaphosphate synthetase I/polynucleotide phosphorylase; Sohlberg, et al. present characterization of two proteins from Streptomyces coelicolor. The protein in this family was shown to have poly(A) polymerase activity and may be responsible for polyadenylating RNA in this species. Reference 2 showed that a nearly identical plasmid-encoded protein from Streptomyces antibioticus is a bifunctional enzyme that acts also as a guanosine pentaphosphate synthetase. Pssm-ID: 131743 [Multi-domain] Cd Length: 719 Bit Score: 502.04 E-value: 1.71e-165
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| PLN00207 | PLN00207 | polyribonucleotide nucleotidyltransferase; Provisional |
22-796 | 2.27e-158 | ||||||||||||
polyribonucleotide nucleotidyltransferase; Provisional Pssm-ID: 215104 [Multi-domain] Cd Length: 891 Bit Score: 489.41 E-value: 2.27e-158
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| RNase_PH_PNPase_2 | cd11364 | Polyribonucleotide nucleotidyltransferase, repeat 2; Polyribonucleotide nucleotidyltransferase ... |
387-614 | 3.33e-138 | ||||||||||||
Polyribonucleotide nucleotidyltransferase, repeat 2; Polyribonucleotide nucleotidyltransferase (PNPase) is a member of the RNase_PH family, named after the bacterial Ribonuclease PH, a 3'-5' exoribonuclease. Structurally, all members of this family form hexameric rings. In the case of PNPase the complex is a trimer, since each monomer contains two tandem copies of the domain. PNPase is involved in mRNA degradation in a 3'-5' direction and in quality control of ribosomal RNA precursors, with the second repeat containing the active site. PNPase is part of the RNA degradosome complex and binds to the scaffolding domain of the endoribonuclease RNase E. Pssm-ID: 206769 [Multi-domain] Cd Length: 223 Bit Score: 412.71 E-value: 3.33e-138
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| RNase_PH_PNPase_1 | cd11363 | Polyribonucleotide nucleotidyltransferase, repeat 1; Polyribonucleotide nucleotidyltransferase ... |
61-295 | 5.82e-120 | ||||||||||||
Polyribonucleotide nucleotidyltransferase, repeat 1; Polyribonucleotide nucleotidyltransferase (PNPase) is a member of the RNase_PH family, named after the bacterial Ribonuclease PH, a 3'-5' exoribonuclease. Structurally, all members of this family form hexameric rings. In the case of PNPase the complex is a trimer, since each monomer contains two tandem copies of the domain. PNPase is involved in mRNA degradation in a 3'-5' direction and in quality control of ribosomal RNA precursors. It is part of the RNA degradosome complex and binds to the scaffolding domain of the endoribonuclease RNase E. Pssm-ID: 206768 [Multi-domain] Cd Length: 229 Bit Score: 365.30 E-value: 5.82e-120
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| RNase_PH | pfam01138 | 3' exoribonuclease family, domain 1; This family includes 3'-5' exoribonucleases. Ribonuclease ... |
387-520 | 2.40e-34 | ||||||||||||
3' exoribonuclease family, domain 1; This family includes 3'-5' exoribonucleases. Ribonuclease PH contains a single copy of this domain, and removes nucleotide residues following the -CCA terminus of tRNA. Polyribonucleotide nucleotidyltransferase (PNPase) contains two tandem copies of the domain. PNPase is involved in mRNA degradation in a 3'-5' direction. The exosome is a 3'-5' exoribonuclease complex that is required for 3' processing of the 5.8S rRNA. Three of its five protein components contain a copy of this domain. A hypothetical protein from S. pombe appears to belong to an uncharacterized subfamily. This subfamily is found in both eukaryotes and archaebacteria. Pssm-ID: 426074 [Multi-domain] Cd Length: 129 Bit Score: 127.71 E-value: 2.40e-34
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| RNase_PH | cd11358 | RNase PH-like 3'-5' exoribonucleases; RNase PH-like 3'-5' exoribonucleases are enzymes that ... |
389-604 | 5.84e-29 | ||||||||||||
RNase PH-like 3'-5' exoribonucleases; RNase PH-like 3'-5' exoribonucleases are enzymes that catalyze the 3' to 5' processing and decay of RNA substrates. Evolutionarily related members can be fond in prokaryotes, archaea, and eukaryotes. Bacterial ribonuclease PH contains a single copy of this domain, and removes nucleotide residues following the -CCA terminus of tRNA. Polyribonucleotide nucleotidyltransferase (PNPase) contains two tandem copies of the domain and is involved in mRNA degradation in a 3'-5' direction. Archaeal exosomes contain two individually encoded RNase PH-like 3'-5' exoribonucleases and are required for 3' processing of the 5.8S rRNA. The eukaryotic exosome core is composed of six individually encoded RNase PH-like subunits, but it is not a phosphorolytic enzyme per se; it directly associates with Rrp44 and Rrp6, which are hydrolytic exoribonucleases related to bacterial RNase II/R and RNase D. All members of the RNase PH-like family form ring structures by oligomerization of six domains or subunits, except for a total of 3 subunits with tandem repeats in the case of PNPase, with a central channel through which the RNA substrate must pass to gain access to the phosphorolytic active sites. Pssm-ID: 206766 [Multi-domain] Cd Length: 218 Bit Score: 115.50 E-value: 5.84e-29
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| RNase_PH | pfam01138 | 3' exoribonuclease family, domain 1; This family includes 3'-5' exoribonucleases. Ribonuclease ... |
68-206 | 2.09e-27 | ||||||||||||
3' exoribonuclease family, domain 1; This family includes 3'-5' exoribonucleases. Ribonuclease PH contains a single copy of this domain, and removes nucleotide residues following the -CCA terminus of tRNA. Polyribonucleotide nucleotidyltransferase (PNPase) contains two tandem copies of the domain. PNPase is involved in mRNA degradation in a 3'-5' direction. The exosome is a 3'-5' exoribonuclease complex that is required for 3' processing of the 5.8S rRNA. Three of its five protein components contain a copy of this domain. A hypothetical protein from S. pombe appears to belong to an uncharacterized subfamily. This subfamily is found in both eukaryotes and archaebacteria. Pssm-ID: 426074 [Multi-domain] Cd Length: 129 Bit Score: 108.06 E-value: 2.09e-27
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| PRK03983 | PRK03983 | exosome complex exonuclease Rrp41; Provisional |
371-604 | 4.93e-25 | ||||||||||||
exosome complex exonuclease Rrp41; Provisional Pssm-ID: 235187 [Multi-domain] Cd Length: 244 Bit Score: 105.10 E-value: 4.93e-25
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| RNase_PH_RRP41 | cd11370 | RRP41 subunit of eukaryotic exosome; The RRP41 subunit of eukaryotic exosome is a member of ... |
377-612 | 1.96e-24 | ||||||||||||
RRP41 subunit of eukaryotic exosome; The RRP41 subunit of eukaryotic exosome is a member of the RNase_PH family, named after the bacterial Ribonuclease PH, a 3'-5' exoribonuclease. Structurally all members of this family form hexameric rings (trimers of Rrp41-Rrp45, Rrp46-Rrp43, and Mtr3-Rrp42 dimers). The eukaryotic exosome core is composed of six individually encoded RNase PH-like subunits and three additional proteins (Rrp4, Csl4 and Rrp40) that form a stable cap and contain RNA-binding domains. The RNase PH-like subunits are no longer phosphorolytic enzymes, the exosome directly associates with Rrp44 and Rrp6, hydrolytic exoribonucleases related to bacterial RNase II/R and RNase D. The exosome plays an important role in RNA turnover. It plays a crucial role in the maturation of stable RNA species such as rRNA, snRNA and snoRNA, quality control of mRNA, and the degradation of RNA processing by-products and non-coding transcripts. Pssm-ID: 206775 [Multi-domain] Cd Length: 226 Bit Score: 102.62 E-value: 1.96e-24
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| RNase_PH_archRRP41 | cd11366 | RRP41 subunit of archaeal exosome; The RRP41 subunit of the archaeal exosome is a member of ... |
387-606 | 5.21e-21 | ||||||||||||
RRP41 subunit of archaeal exosome; The RRP41 subunit of the archaeal exosome is a member of the RNase_PH family, named after the bacterial Ribonuclease PH, a 3'-5' exoribonuclease. Structurally all members of this family form hexameric rings (trimers of dimers). In archaea, the ring is formed by three Rrp41:Rrp42 dimers. The central chamber within the ring contains three phosphorolytic active sites located in an Rrp41 pocket at the interface between Rrp42 and Rrp41. The ring is capped by three copies of Rrp4 and/or Csl4 which contain putative RNA interaction domains. The archaeal exosome degrades single-stranded RNA (ssRNA) in the 3'-5' direction, but also can catalyze the reverse reaction of adding nucleoside diphosphates to the 3'-end of RNA which has been shown to lead to the formation of poly-A-rich tails on RNA. Pssm-ID: 206771 [Multi-domain] Cd Length: 214 Bit Score: 92.40 E-value: 5.21e-21
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| PNPase | pfam03726 | Polyribonucleotide nucleotidyltransferase, RNA binding domain; This family contains the RNA ... |
305-383 | 7.79e-17 | ||||||||||||
Polyribonucleotide nucleotidyltransferase, RNA binding domain; This family contains the RNA binding domain of Polyribonucleotide nucleotidyltransferase (PNPase) PNPase is involved in mRNA degradation in a 3'-5' direction. Pssm-ID: 397682 [Multi-domain] Cd Length: 80 Bit Score: 76.17 E-value: 7.79e-17
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| S1_PNPase | cd04472 | S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a ... |
689-755 | 2.85e-16 | ||||||||||||
S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA. It is a trimeric multidomain protein. The C-terminus contains the S1 domain which binds ssRNA. This family is classified based on the S1 domain. PNPase nonspecifically removes the 3' nucleotides from mRNA, but is stalled by double-stranded RNA structures such as a stem-loop. Evidence shows that a minimum of 7-10 unpaired nucleotides at the 3' end, is required for PNPase degradation. It is suggested that PNPase also dephosphorylates the RNA 5' end. This additional activity may regulate the 5'-dependent activity of RNaseE in vivo. Pssm-ID: 239918 [Multi-domain] Cd Length: 68 Bit Score: 74.12 E-value: 2.85e-16
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| YabR | COG1098 | Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function ... |
685-781 | 4.22e-13 | ||||||||||||
Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function prediction only]; Pssm-ID: 440715 [Multi-domain] Cd Length: 130 Bit Score: 67.13 E-value: 4.22e-13
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| S1 | smart00316 | Ribosomal protein S1-like RNA-binding domain; |
687-757 | 1.12e-11 | ||||||||||||
Ribosomal protein S1-like RNA-binding domain; Pssm-ID: 197648 [Multi-domain] Cd Length: 72 Bit Score: 61.08 E-value: 1.12e-11
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| S1_dom_CvfD | NF040579 | CvfD/Ygs/GSP13 family RNA-binding post-transcriptional regulator; CvfD, Ygs, and GSP13 form a ... |
686-767 | 5.84e-11 | ||||||||||||
CvfD/Ygs/GSP13 family RNA-binding post-transcriptional regulator; CvfD, Ygs, and GSP13 form a family of full-length homologs of RNA-binding proteins from the Firmicutes with a single copy of the S1 domain. Several members of the family have been characterized as general stress proteins, and the most recently characterized, CvfD, was shown to act as a post-transcriptional regulator. Pssm-ID: 468553 [Multi-domain] Cd Length: 113 Bit Score: 60.52 E-value: 5.84e-11
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| S1_RPS1_repeat_hs4 | cd05692 | S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ... |
694-757 | 7.07e-11 | ||||||||||||
S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (hs4) of the H. sapiens RPS1 homolog. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog. Pssm-ID: 240197 [Multi-domain] Cd Length: 69 Bit Score: 58.84 E-value: 7.07e-11
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| RNase_PH_bact | cd11362 | Ribonuclease PH; Ribonuclease PH (RNase PH)-like 3'-5' exoribonucleases are enzymes that ... |
403-572 | 9.55e-11 | ||||||||||||
Ribonuclease PH; Ribonuclease PH (RNase PH)-like 3'-5' exoribonucleases are enzymes that catalyze the 3' to 5' processing and decay of RNA substrates. Structurally all members of this family form hexameric rings (trimers of dimers). Bacterial RNase PH forms a homohexameric ring, and removes nucleotide residues following the -CCA terminus of tRNA. Pssm-ID: 206767 [Multi-domain] Cd Length: 227 Bit Score: 62.63 E-value: 9.55e-11
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| PRK08059 | PRK08059 | general stress protein 13; Validated |
686-767 | 1.11e-10 | ||||||||||||
general stress protein 13; Validated Pssm-ID: 181215 [Multi-domain] Cd Length: 123 Bit Score: 60.06 E-value: 1.11e-10
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| Rph | COG0689 | Ribonuclease PH [Translation, ribosomal structure and biogenesis]; |
379-533 | 4.38e-10 | ||||||||||||
Ribonuclease PH [Translation, ribosomal structure and biogenesis]; Pssm-ID: 440453 [Multi-domain] Cd Length: 238 Bit Score: 61.20 E-value: 4.38e-10
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| RNase_PH_C | pfam03725 | 3' exoribonuclease family, domain 2; This family includes 3'-5' exoribonucleases. Ribonuclease ... |
209-273 | 1.13e-09 | ||||||||||||
3' exoribonuclease family, domain 2; This family includes 3'-5' exoribonucleases. Ribonuclease PH contains a single copy of this domain, and removes nucleotide residues following the -CCA terminus of tRNA. Polyribonucleotide nucleotidyltransferase (PNPase) contains two tandem copies of the domain. PNPase is involved in mRNA degradation in a 3'-5' direction. The exosome is a 3'-5' exoribonuclease complex that is required for 3' processing of the 5.8S rRNA. Three of its five protein components, Swiss:P46948 Swiss:Q12277 and Swiss:P25359 contain a copy of this domain. Swiss:Q10205, a hypothetical protein from S. pombe appears to belong to an uncharacterized subfamily. This subfamily is found in both eukaryotes and archaebacteria. Pssm-ID: 427466 [Multi-domain] Cd Length: 67 Bit Score: 55.28 E-value: 1.13e-09
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| RNase_PH_MTR3 | cd11371 | MTR3 subunit of eukaryotic exosome; The MTR3 subunit of eukaryotic exosome is a member of the ... |
388-545 | 1.60e-09 | ||||||||||||
MTR3 subunit of eukaryotic exosome; The MTR3 subunit of eukaryotic exosome is a member of the RNase_PH family, named after the bacterial Ribonuclease PH, a 3'-5' exoribonuclease. Structurally all members of this family form hexameric rings (trimers of Rrp41-Rrp45, Rrp46-Rrp43, and Mtr3-Rrp42 dimers). The eukaryotic exosome core is composed of six individually encoded RNase PH-like subunits and three additional proteins (Rrp4, Csl4 and Rrp40) that form a stable cap and contain RNA-binding domains. The RNase PH-like subunits are no longer phosphorolytic enzymes, the exosome directly associates with Rrp44 and Rrp6, hydrolytic exoribonucleases related to bacterial RNase II/R and RNase D. The exosome plays an important role in RNA turnover. It plays a crucial role in the maturation of stable RNA species such as rRNA, snRNA and snoRNA, quality control of mRNA, and the degradation of RNA processing by-products and non-coding transcripts. Pssm-ID: 206776 [Multi-domain] Cd Length: 210 Bit Score: 58.73 E-value: 1.60e-09
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| RpsA | COG0539 | Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ... |
672-762 | 3.74e-09 | ||||||||||||
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 is part of the Pathway/BioSystem: Ribosome 30S subunit Pssm-ID: 440305 [Multi-domain] Cd Length: 348 Bit Score: 59.67 E-value: 3.74e-09
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| RNase_PH_RRP46 | cd11372 | RRP46 subunit of eukaryotic exosome; The RRP46 subunit of eukaryotic exosome is a member of ... |
389-535 | 4.99e-09 | ||||||||||||
RRP46 subunit of eukaryotic exosome; The RRP46 subunit of eukaryotic exosome is a member of the RNase_PH family, named after the bacterial Ribonuclease PH, a 3'-5' exoribonuclease. Structurally all members of this family form hexameric rings (trimers of Rrp41-Rrp45, Rrp46-Rrp43, and Mtr3-Rrp42 dimers). The eukaryotic exosome core is composed of six individually encoded RNase PH-like subunits and three additional proteins (Rrp4, Csl4 and Rrp40) that form a stable cap and contain RNA-binding domains. The RNase PH-like subunits are no longer phosphorolytic enzymes, the exosome directly associates with Rrp44 and Rrp6, hydrolytic exoribonucleases related to bacterial RNase II/R and RNase D. The exosome plays an important role in RNA turnover. It plays a crucial role in the maturation of stable RNA species such as rRNA, snRNA and snoRNA, quality control of mRNA, and the degradation of RNA processing by-products and non-coding transcripts. Pssm-ID: 206777 [Multi-domain] Cd Length: 199 Bit Score: 57.19 E-value: 4.99e-09
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| rph | PRK00173 | ribonuclease PH; Reviewed |
379-533 | 7.98e-09 | ||||||||||||
ribonuclease PH; Reviewed Pssm-ID: 178914 Cd Length: 238 Bit Score: 57.43 E-value: 7.98e-09
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| rpsA | PRK06676 | 30S ribosomal protein S1; Reviewed |
673-761 | 1.14e-08 | ||||||||||||
30S ribosomal protein S1; Reviewed Pssm-ID: 235851 [Multi-domain] Cd Length: 390 Bit Score: 58.35 E-value: 1.14e-08
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| Rrp42 | COG2123 | Exosome complex RNA-binding protein Rrp42, RNase PH superfamily [Intracellular trafficking, ... |
361-423 | 2.88e-08 | ||||||||||||
Exosome complex RNA-binding protein Rrp42, RNase PH superfamily [Intracellular trafficking, secretion, and vesicular transport]; Pssm-ID: 441726 [Multi-domain] Cd Length: 264 Bit Score: 55.96 E-value: 2.88e-08
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| S1_like | cd00164 | S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ... |
692-755 | 6.36e-08 | ||||||||||||
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold. Pssm-ID: 238094 [Multi-domain] Cd Length: 65 Bit Score: 50.07 E-value: 6.36e-08
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| PRK00087 | PRK00087 | bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1; |
673-761 | 9.84e-08 | ||||||||||||
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1; Pssm-ID: 234623 [Multi-domain] Cd Length: 647 Bit Score: 56.11 E-value: 9.84e-08
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| S1_DHX8_helicase | cd05684 | S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH ... |
689-723 | 1.32e-07 | ||||||||||||
S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH (Asp-Glu-Ala-His) box polypeptide. The DEAH-box RNA helicases are thought to play key roles in pre-mRNA splicing and DHX8 facilitates nuclear export of spliced mRNA by releasing the RNA from the spliceosome. DHX8 is also known as HRH1 (human RNA helicase 1) in Homo sapiens and PRP22 in Saccharomyces cerevisiae. Pssm-ID: 240189 [Multi-domain] Cd Length: 79 Bit Score: 49.93 E-value: 1.32e-07
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| PRK08582 | PRK08582 | RNA-binding protein S1; |
686-722 | 1.52e-07 | ||||||||||||
RNA-binding protein S1; Pssm-ID: 236305 [Multi-domain] Cd Length: 139 Bit Score: 51.57 E-value: 1.52e-07
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| PRK04282 | PRK04282 | exosome complex protein Rrp42; |
361-423 | 1.79e-07 | ||||||||||||
exosome complex protein Rrp42; Pssm-ID: 235268 [Multi-domain] Cd Length: 271 Bit Score: 53.73 E-value: 1.79e-07
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| S1_RPS1_repeat_ec3 | cd05688 | S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ... |
688-722 | 2.43e-07 | ||||||||||||
S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 3 (ec3) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog. Pssm-ID: 240193 [Multi-domain] Cd Length: 68 Bit Score: 48.78 E-value: 2.43e-07
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| S1_RecJ_like | cd04473 | S1_RecJ_like: The S1 domain of the archaea-specific RecJ-like exonuclease. The function of ... |
684-722 | 2.92e-07 | ||||||||||||
S1_RecJ_like: The S1 domain of the archaea-specific RecJ-like exonuclease. The function of this family is not fully understood. In Escherichia coli, RecJ degrades single-stranded DNA in the 5'-3' direction and participates in homologous recombination and mismatch repair. Pssm-ID: 239919 [Multi-domain] Cd Length: 77 Bit Score: 48.76 E-value: 2.92e-07
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| RNase_PH_PNPase_1 | cd11363 | Polyribonucleotide nucleotidyltransferase, repeat 1; Polyribonucleotide nucleotidyltransferase ... |
402-610 | 3.29e-07 | ||||||||||||
Polyribonucleotide nucleotidyltransferase, repeat 1; Polyribonucleotide nucleotidyltransferase (PNPase) is a member of the RNase_PH family, named after the bacterial Ribonuclease PH, a 3'-5' exoribonuclease. Structurally, all members of this family form hexameric rings. In the case of PNPase the complex is a trimer, since each monomer contains two tandem copies of the domain. PNPase is involved in mRNA degradation in a 3'-5' direction and in quality control of ribosomal RNA precursors. It is part of the RNA degradosome complex and binds to the scaffolding domain of the endoribonuclease RNase E. Pssm-ID: 206768 [Multi-domain] Cd Length: 229 Bit Score: 52.13 E-value: 3.29e-07
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| RNase_PH_archRRP42 | cd11365 | RRP42 subunit of archaeal exosome; The RRP42 subunit of the archaeal exosome is a member of ... |
362-421 | 4.32e-07 | ||||||||||||
RRP42 subunit of archaeal exosome; The RRP42 subunit of the archaeal exosome is a member of the RNase_PH family, named after the bacterial Ribonuclease PH, a 3'-5' exoribonuclease. Structurally all members of this family form hexameric rings (trimers of dimers). In archaea, the ring is formed by three Rrp41:Rrp42 dimers. The central chamber within the ring contains three phosphorolytic active sites located in an Rrp41 pocket at the interface between Rrp42 and Rrp41. The ring is capped by three copies of Rrp4 and/or Csl4 which contain putative RNA interaction domains. The archaeal exosome degrades single-stranded RNA (ssRNA) in the 3'-5' direction, but also can catalyze the reverse reaction of adding nucleoside diphosphates to the 3'-end of RNA which has been shown to lead to the formation of poly-A-rich tails on RNA. It is required for 3' processing of the 5.8S rRNA. Pssm-ID: 206770 [Multi-domain] Cd Length: 256 Bit Score: 52.22 E-value: 4.32e-07
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| rpsA | PRK07899 | 30S ribosomal protein S1; Reviewed |
679-759 | 8.07e-07 | ||||||||||||
30S ribosomal protein S1; Reviewed Pssm-ID: 236126 [Multi-domain] Cd Length: 486 Bit Score: 52.74 E-value: 8.07e-07
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| rpsA | PRK06299 | 30S ribosomal protein S1; Reviewed |
682-722 | 9.67e-07 | ||||||||||||
30S ribosomal protein S1; Reviewed Pssm-ID: 235775 [Multi-domain] Cd Length: 565 Bit Score: 52.47 E-value: 9.67e-07
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| PRK07400 | PRK07400 | 30S ribosomal protein S1; Reviewed |
681-761 | 1.39e-06 | ||||||||||||
30S ribosomal protein S1; Reviewed Pssm-ID: 180960 [Multi-domain] Cd Length: 318 Bit Score: 51.34 E-value: 1.39e-06
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| S1_pNO40 | cd05686 | S1_pNO40: pNO40 , S1-like RNA-binding domain. pNO40 is a nucleolar protein of unknown function ... |
687-757 | 1.51e-06 | ||||||||||||
S1_pNO40: pNO40 , S1-like RNA-binding domain. pNO40 is a nucleolar protein of unknown function with an N-terminal S1 RNA binding domain, a CCHC type zinc finger, and clusters of basic amino acids representing a potential nucleolar targeting signal. pNO40 was identified through a yeast two-hybrid interaction screen of a human kidney cDNA library using the pinin (pnn) protein as bait. pNO40 is thought to play a role in ribosome maturation and/or biogenesis. Pssm-ID: 240191 [Multi-domain] Cd Length: 73 Bit Score: 46.71 E-value: 1.51e-06
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| RNase_PH_RRP46 | cd11372 | RRP46 subunit of eukaryotic exosome; The RRP46 subunit of eukaryotic exosome is a member of ... |
83-278 | 1.68e-06 | ||||||||||||
RRP46 subunit of eukaryotic exosome; The RRP46 subunit of eukaryotic exosome is a member of the RNase_PH family, named after the bacterial Ribonuclease PH, a 3'-5' exoribonuclease. Structurally all members of this family form hexameric rings (trimers of Rrp41-Rrp45, Rrp46-Rrp43, and Mtr3-Rrp42 dimers). The eukaryotic exosome core is composed of six individually encoded RNase PH-like subunits and three additional proteins (Rrp4, Csl4 and Rrp40) that form a stable cap and contain RNA-binding domains. The RNase PH-like subunits are no longer phosphorolytic enzymes, the exosome directly associates with Rrp44 and Rrp6, hydrolytic exoribonucleases related to bacterial RNase II/R and RNase D. The exosome plays an important role in RNA turnover. It plays a crucial role in the maturation of stable RNA species such as rRNA, snRNA and snoRNA, quality control of mRNA, and the degradation of RNA processing by-products and non-coding transcripts. Pssm-ID: 206777 [Multi-domain] Cd Length: 199 Bit Score: 49.87 E-value: 1.68e-06
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| RpsA | COG0539 | Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ... |
682-723 | 1.70e-06 | ||||||||||||
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 is part of the Pathway/BioSystem: Ribosome 30S subunit Pssm-ID: 440305 [Multi-domain] Cd Length: 348 Bit Score: 51.20 E-value: 1.70e-06
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| KH-I_PNPase | cd02393 | type I K homology (KH) RNA-binding domain found in polyribonucleotide nucleotidyltransferase ... |
644-687 | 2.25e-06 | ||||||||||||
type I K homology (KH) RNA-binding domain found in polyribonucleotide nucleotidyltransferase (PNPase) and similar proteins; PNPase, also called polynucleotide phosphorylase, is a polyribonucleotide nucleotidyl transferase that degrades mRNA in prokaryotes and plant chloroplasts. It catalyzes the phosphorolysis of single-stranded polyribonucleotides processively in the 3'- to 5'-direction. It is also involved, along with RNase II, in tRNA processing. The C-terminal region of PNPase contains domains homologous to those in other RNA binding proteins: a KH domain and an S1 domain. The model corresponds to the KH domain. Pssm-ID: 411803 [Multi-domain] Cd Length: 70 Bit Score: 45.93 E-value: 2.25e-06
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| S1 | smart00316 | Ribosomal protein S1-like RNA-binding domain; |
918-980 | 8.55e-06 | ||||||||||||
Ribosomal protein S1-like RNA-binding domain; Pssm-ID: 197648 [Multi-domain] Cd Length: 72 Bit Score: 44.52 E-value: 8.55e-06
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| rpsA | TIGR00717 | ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ... |
688-757 | 1.30e-05 | ||||||||||||
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found in most bacterial genomes in a single copy, but is not present in the Mycoplasmas. It is heterogeneous with respect to the number of repeats of the S1 RNA binding domain described by pfam00575: six repeats in E. coli and most other bacteria, four in Bacillus subtilis and some other species. rpsA is an essential gene in E. coli but not in B. subtilis. It is associated with the cytidylate kinase gene cmk in many species, and fused to it in Treponema pallidum. RpsA is proposed (Medline:97323001) to assist in mRNA degradation. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned. [Protein synthesis, Ribosomal proteins: synthesis and modification] Pssm-ID: 273232 [Multi-domain] Cd Length: 516 Bit Score: 48.96 E-value: 1.30e-05
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| S1 | pfam00575 | S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ... |
687-756 | 1.31e-05 | ||||||||||||
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is structurally similar to cold shock protein which binds nucleic acids. The S1 domain has an OB-fold structure. Pssm-ID: 425760 [Multi-domain] Cd Length: 72 Bit Score: 43.82 E-value: 1.31e-05
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| COG1107 | COG1107 | Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [Replication, ... |
685-721 | 1.52e-05 | ||||||||||||
Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [Replication, recombination and repair]; Pssm-ID: 440724 [Multi-domain] Cd Length: 626 Bit Score: 48.68 E-value: 1.52e-05
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| rpsA | TIGR00717 | ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ... |
686-766 | 1.55e-05 | ||||||||||||
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found in most bacterial genomes in a single copy, but is not present in the Mycoplasmas. It is heterogeneous with respect to the number of repeats of the S1 RNA binding domain described by pfam00575: six repeats in E. coli and most other bacteria, four in Bacillus subtilis and some other species. rpsA is an essential gene in E. coli but not in B. subtilis. It is associated with the cytidylate kinase gene cmk in many species, and fused to it in Treponema pallidum. RpsA is proposed (Medline:97323001) to assist in mRNA degradation. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned. [Protein synthesis, Ribosomal proteins: synthesis and modification] Pssm-ID: 273232 [Multi-domain] Cd Length: 516 Bit Score: 48.58 E-value: 1.55e-05
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| RNase_PH_archRRP41 | cd11366 | RRP41 subunit of archaeal exosome; The RRP41 subunit of the archaeal exosome is a member of ... |
70-292 | 2.52e-05 | ||||||||||||
RRP41 subunit of archaeal exosome; The RRP41 subunit of the archaeal exosome is a member of the RNase_PH family, named after the bacterial Ribonuclease PH, a 3'-5' exoribonuclease. Structurally all members of this family form hexameric rings (trimers of dimers). In archaea, the ring is formed by three Rrp41:Rrp42 dimers. The central chamber within the ring contains three phosphorolytic active sites located in an Rrp41 pocket at the interface between Rrp42 and Rrp41. The ring is capped by three copies of Rrp4 and/or Csl4 which contain putative RNA interaction domains. The archaeal exosome degrades single-stranded RNA (ssRNA) in the 3'-5' direction, but also can catalyze the reverse reaction of adding nucleoside diphosphates to the 3'-end of RNA which has been shown to lead to the formation of poly-A-rich tails on RNA. Pssm-ID: 206771 [Multi-domain] Cd Length: 214 Bit Score: 46.56 E-value: 2.52e-05
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| S1_Tex | cd05685 | S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has ... |
689-755 | 3.53e-05 | ||||||||||||
S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has been characterized in Bordetella pertussis and Pseudomonas aeruginosa. The tex gene is essential in Bortella pertusis and is named for its role in toxin expression. Tex has two functional domains, an N-terminal domain homologous to the Escherichia coli maltose repression protein, which is a poorly defined transcriptional factor, and a C-terminal S1 RNA-binding domain. Tex is found in prokaryotes, eukaryotes, and archaea. Pssm-ID: 240190 [Multi-domain] Cd Length: 68 Bit Score: 42.61 E-value: 3.53e-05
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| PRK07252 | PRK07252 | S1 RNA-binding domain-containing protein; |
686-721 | 3.54e-05 | ||||||||||||
S1 RNA-binding domain-containing protein; Pssm-ID: 180908 [Multi-domain] Cd Length: 120 Bit Score: 44.31 E-value: 3.54e-05
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| rpsA | PRK06299 | 30S ribosomal protein S1; Reviewed |
688-771 | 4.21e-05 | ||||||||||||
30S ribosomal protein S1; Reviewed Pssm-ID: 235775 [Multi-domain] Cd Length: 565 Bit Score: 47.47 E-value: 4.21e-05
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| RNase_PH_RRP45 | cd11368 | RRP45 subunit of eukaryotic exosome; The RRP45 subunit of eukaryotic exosome is a member of ... |
374-419 | 6.97e-05 | ||||||||||||
RRP45 subunit of eukaryotic exosome; The RRP45 subunit of eukaryotic exosome is a member of the RNase_PH family, named after the bacterial Ribonuclease PH, a 3'-5' exoribonuclease. Structurally all members of this family form hexameric rings (trimers of Rrp41-Rrp45, Rrp46-Rrp43, and Mtr3-Rrp42 dimers). The eukaryotic exosome core is composed of six individually encoded RNase PH-like subunits and three additional proteins (Rrp4, Csl4 and Rrp40) that form a stable cap and contain RNA-binding domains. The RNase PH-like subunits are no longer phosphorolytic enzymes, the exosome directly associates with Rrp44 and Rrp6, hydrolytic exoribonucleases related to bacterial RNase II/R and RNase D. The exosome plays an important role in RNA turnover. It plays a crucial role in the maturation of stable RNA species such as rRNA, snRNA and snoRNA, quality control of mRNA, and the degradation of RNA processing by-products and non-coding transcripts. Pssm-ID: 206773 [Multi-domain] Cd Length: 259 Bit Score: 45.60 E-value: 6.97e-05
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| rpsA | PRK06299 | 30S ribosomal protein S1; Reviewed |
688-722 | 1.47e-04 | ||||||||||||
30S ribosomal protein S1; Reviewed Pssm-ID: 235775 [Multi-domain] Cd Length: 565 Bit Score: 45.54 E-value: 1.47e-04
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| rpsA | PRK06299 | 30S ribosomal protein S1; Reviewed |
686-723 | 1.47e-04 | ||||||||||||
30S ribosomal protein S1; Reviewed Pssm-ID: 235775 [Multi-domain] Cd Length: 565 Bit Score: 45.54 E-value: 1.47e-04
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| PRK05807 | PRK05807 | RNA-binding protein S1; |
686-767 | 1.70e-04 | ||||||||||||
RNA-binding protein S1; Pssm-ID: 235614 [Multi-domain] Cd Length: 136 Bit Score: 42.43 E-value: 1.70e-04
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| S1_RPS1_repeat_ec5 | cd05690 | S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ... |
689-722 | 2.40e-04 | ||||||||||||
S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 5 (ec5) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog. Pssm-ID: 240195 [Multi-domain] Cd Length: 69 Bit Score: 40.17 E-value: 2.40e-04
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| S1_Rrp5_repeat_hs6_sc5 | cd05698 | S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ... |
694-757 | 2.99e-04 | ||||||||||||
S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 6 (hs6) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea. Pssm-ID: 240203 [Multi-domain] Cd Length: 70 Bit Score: 39.90 E-value: 2.99e-04
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| S1_Rrp5_repeat_hs8_sc7 | cd04461 | S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 ... |
685-722 | 4.21e-04 | ||||||||||||
S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 repeat 7 (sc7)-like domains. Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in S. cerevisiae Rrp5 and 14 S1 repeats in H. sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 8 and S. cerevisiae S1 repeat 7. Rrp5 is found in eukaryotes but not in prokaryotes or archaea. Pssm-ID: 239908 [Multi-domain] Cd Length: 83 Bit Score: 39.88 E-value: 4.21e-04
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| rpsA | TIGR00717 | ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ... |
685-773 | 6.19e-04 | ||||||||||||
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found in most bacterial genomes in a single copy, but is not present in the Mycoplasmas. It is heterogeneous with respect to the number of repeats of the S1 RNA binding domain described by pfam00575: six repeats in E. coli and most other bacteria, four in Bacillus subtilis and some other species. rpsA is an essential gene in E. coli but not in B. subtilis. It is associated with the cytidylate kinase gene cmk in many species, and fused to it in Treponema pallidum. RpsA is proposed (Medline:97323001) to assist in mRNA degradation. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned. [Protein synthesis, Ribosomal proteins: synthesis and modification] Pssm-ID: 273232 [Multi-domain] Cd Length: 516 Bit Score: 43.57 E-value: 6.19e-04
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| rpsA | PRK06676 | 30S ribosomal protein S1; Reviewed |
682-723 | 6.78e-04 | ||||||||||||
30S ribosomal protein S1; Reviewed Pssm-ID: 235851 [Multi-domain] Cd Length: 390 Bit Score: 43.33 E-value: 6.78e-04
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| rpsA | PRK07899 | 30S ribosomal protein S1; Reviewed |
688-776 | 7.32e-04 | ||||||||||||
30S ribosomal protein S1; Reviewed Pssm-ID: 236126 [Multi-domain] Cd Length: 486 Bit Score: 43.11 E-value: 7.32e-04
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| PRK00087 | PRK00087 | bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1; |
688-723 | 8.98e-04 | ||||||||||||
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1; Pssm-ID: 234623 [Multi-domain] Cd Length: 647 Bit Score: 43.01 E-value: 8.98e-04
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| RNase_PH_RRP43 | cd11369 | RRP43 subunit of eukaryotic exosome; The RRP43 subunit of eukaryotic exosome is a member of ... |
371-420 | 1.01e-03 | ||||||||||||
RRP43 subunit of eukaryotic exosome; The RRP43 subunit of eukaryotic exosome is a member of the RNase_PH family, named after the bacterial Ribonuclease PH, a 3'-5' exoribonuclease. Structurally all members of this family form hexameric rings (trimers of Rrp41-Rrp45, Rrp46-Rrp43, and Mtr3-Rrp42 dimers). The eukaryotic exosome core is composed of six individually encoded RNase PH-like subunits and three additional proteins (Rrp4, Csl4 and Rrp40) that form a stable cap and contain RNA-binding domains. The RNase PH-like subunits are no longer phosphorolytic enzymes, the exosome directly associates with Rrp44 and Rrp6, hydrolytic exoribonucleases related to bacterial RNase II/R and RNase D. The exosome plays an important role in RNA turnover. It plays a crucial role in the maturation of stable RNA species such as rRNA, snRNA and snoRNA, quality control of mRNA, and the degradation of RNA processing by-products and non-coding transcripts. Pssm-ID: 206774 [Multi-domain] Cd Length: 261 Bit Score: 42.16 E-value: 1.01e-03
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| S1_Rrp5_repeat_sc12 | cd05708 | S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ... |
687-722 | 1.43e-03 | ||||||||||||
S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 12 (sc12). Rrp5 is found in eukaryotes but not in prokaryotes or archaea. Pssm-ID: 240213 [Multi-domain] Cd Length: 77 Bit Score: 38.46 E-value: 1.43e-03
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| S1_IF2_alpha | cd04452 | S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain. ... |
687-757 | 1.88e-03 | ||||||||||||
S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Eukaryotic and archaeal Initiation Factor 2 (e- and aIF2, respectively) are heterotrimeric proteins with three subunits (alpha, beta, and gamma). IF2 plays a crucial role in the process of translation initiation. The IF2 gamma subunit contains a GTP-binding site. The IF2 beta and gamma subunits together are thought to be responsible for binding methionyl-initiator tRNA. The ternary complex consisting of IF2, GTP, and the methionyl-initiator tRNA binds to the small subunit of the ribosome, as part of a pre-initiation complex that scans the mRNA to find the AUG start codon. The IF2-bound GTP is hydrolyzed to GDP when the methionyl-initiator tRNA binds the AUG start codon, at which time the IF2 is released with its bound GDP. The large ribosomal subunit then joins with the small subunit to complete the initiation complex, which is competent to begin translation. The IF2a subunit is a major site of control of the translation initiation process, via phosphorylation of a specific serine residue. This alpha subunit is well conserved in eukaryotes and archaea but is not present in bacteria. IF2 is a cold-shock-inducible protein. Pssm-ID: 239899 [Multi-domain] Cd Length: 76 Bit Score: 37.95 E-value: 1.88e-03
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| rpsA | PRK13806 | 30S ribosomal protein S1; Provisional |
682-723 | 1.96e-03 | ||||||||||||
30S ribosomal protein S1; Provisional Pssm-ID: 237516 [Multi-domain] Cd Length: 491 Bit Score: 42.02 E-value: 1.96e-03
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| rpsA | PRK13806 | 30S ribosomal protein S1; Provisional |
685-722 | 4.06e-03 | ||||||||||||
30S ribosomal protein S1; Provisional Pssm-ID: 237516 [Multi-domain] Cd Length: 491 Bit Score: 40.86 E-value: 4.06e-03
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| S1_RPS1_repeat_ec4 | cd05689 | S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ... |
694-721 | 4.70e-03 | ||||||||||||
S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (ec4) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog. Pssm-ID: 240194 [Multi-domain] Cd Length: 72 Bit Score: 36.79 E-value: 4.70e-03
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| PRK08059 | PRK08059 | general stress protein 13; Validated |
913-966 | 4.76e-03 | ||||||||||||
general stress protein 13; Validated Pssm-ID: 181215 [Multi-domain] Cd Length: 123 Bit Score: 38.10 E-value: 4.76e-03
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| PRK03983 | PRK03983 | exosome complex exonuclease Rrp41; Provisional |
70-292 | 5.32e-03 | ||||||||||||
exosome complex exonuclease Rrp41; Provisional Pssm-ID: 235187 [Multi-domain] Cd Length: 244 Bit Score: 39.62 E-value: 5.32e-03
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