polyribonucleotide nucleotidyltransferase [Oribacterium asaccharolyticum ACB7]
Protein Classification
polyribonucleotide nucleotidyltransferase( domain architecture ID 11485531)
polyribonucleotide nucleotidyltransferase 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 endoribonuclease RNase E
List of domain hits
| Name | Accession | Description | Interval | E-value | ||||||||||
| Pnp | COG1185 | Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ... |
4-691 | 0e+00 | ||||||||||
Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]; : Pssm-ID: 440798 [Multi-domain] Cd Length: 686 Bit Score: 1140.50 E-value: 0e+00
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| Name | Accession | Description | Interval | E-value | ||||||||||
| Pnp | COG1185 | Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ... |
4-691 | 0e+00 | ||||||||||
Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]; Pssm-ID: 440798 [Multi-domain] Cd Length: 686 Bit Score: 1140.50 E-value: 0e+00
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| PRK11824 | PRK11824 | polynucleotide phosphorylase/polyadenylase; Provisional |
1-691 | 0e+00 | ||||||||||
polynucleotide phosphorylase/polyadenylase; Provisional Pssm-ID: 236995 [Multi-domain] Cd Length: 693 Bit Score: 1108.58 E-value: 0e+00
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| polynuc_phos | TIGR03591 | polyribonucleotide nucleotidyltransferase; Members of this protein family are ... |
8-691 | 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: 999.33 E-value: 0e+00
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| RNase_PH_PNPase_2 | cd11364 | Polyribonucleotide nucleotidyltransferase, repeat 2; Polyribonucleotide nucleotidyltransferase ... |
320-545 | 2.25e-129 | ||||||||||
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: 381.51 E-value: 2.25e-129
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| RNase_PH | pfam01138 | 3' exoribonuclease family, domain 1; This family includes 3'-5' exoribonucleases. Ribonuclease ... |
320-454 | 2.66e-24 | ||||||||||
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: 98.43 E-value: 2.66e-24
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| S1 | smart00316 | Ribosomal protein S1-like RNA-binding domain; |
621-691 | 4.81e-21 | ||||||||||
Ribosomal protein S1-like RNA-binding domain; Pssm-ID: 197648 [Multi-domain] Cd Length: 72 Bit Score: 87.27 E-value: 4.81e-21
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| S1_dom_CvfD | NF040579 | CvfD/Ygs/GSP13 family RNA-binding post-transcriptional regulator; CvfD, Ygs, and GSP13 form a ... |
620-691 | 2.44e-17 | ||||||||||
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: 78.24 E-value: 2.44e-17
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| Name | Accession | Description | Interval | E-value | |||||||||||
| Pnp | COG1185 | Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ... |
4-691 | 0e+00 | |||||||||||
Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]; Pssm-ID: 440798 [Multi-domain] Cd Length: 686 Bit Score: 1140.50 E-value: 0e+00
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| PRK11824 | PRK11824 | polynucleotide phosphorylase/polyadenylase; Provisional |
1-691 | 0e+00 | |||||||||||
polynucleotide phosphorylase/polyadenylase; Provisional Pssm-ID: 236995 [Multi-domain] Cd Length: 693 Bit Score: 1108.58 E-value: 0e+00
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| polynuc_phos | TIGR03591 | polyribonucleotide nucleotidyltransferase; Members of this protein family are ... |
8-691 | 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: 999.33 E-value: 0e+00
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| pppGpp_PNP | TIGR02696 | guanosine pentaphosphate synthetase I/polynucleotide phosphorylase; Sohlberg, et al. present ... |
12-688 | 0e+00 | |||||||||||
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: 636.09 E-value: 0e+00
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| PLN00207 | PLN00207 | polyribonucleotide nucleotidyltransferase; Provisional |
12-691 | 0e+00 | |||||||||||
polyribonucleotide nucleotidyltransferase; Provisional Pssm-ID: 215104 [Multi-domain] Cd Length: 891 Bit Score: 560.28 E-value: 0e+00
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| RNase_PH_PNPase_2 | cd11364 | Polyribonucleotide nucleotidyltransferase, repeat 2; Polyribonucleotide nucleotidyltransferase ... |
320-545 | 2.25e-129 | |||||||||||
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: 381.51 E-value: 2.25e-129
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| RNase_PH_PNPase_1 | cd11363 | Polyribonucleotide nucleotidyltransferase, repeat 1; Polyribonucleotide nucleotidyltransferase ... |
3-231 | 3.75e-103 | |||||||||||
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: 314.46 E-value: 3.75e-103
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| S1_PNPase | cd04472 | S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a ... |
623-690 | 8.78e-29 | |||||||||||
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: 109.17 E-value: 8.78e-29
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| YabR | COG1098 | Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function ... |
619-691 | 1.99e-27 | |||||||||||
Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function prediction only]; Pssm-ID: 440715 [Multi-domain] Cd Length: 130 Bit Score: 107.57 E-value: 1.99e-27
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| KH-I_PNPase | cd02393 | type I K homology (KH) RNA-binding domain found in polyribonucleotide nucleotidyltransferase ... |
552-621 | 1.60e-26 | |||||||||||
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: 102.94 E-value: 1.60e-26
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| RNase_PH | pfam01138 | 3' exoribonuclease family, domain 1; This family includes 3'-5' exoribonucleases. Ribonuclease ... |
320-454 | 2.66e-24 | |||||||||||
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: 98.43 E-value: 2.66e-24
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| RNase_PH | pfam01138 | 3' exoribonuclease family, domain 1; This family includes 3'-5' exoribonucleases. Ribonuclease ... |
24-142 | 6.95e-24 | |||||||||||
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: 97.28 E-value: 6.95e-24
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| PRK03983 | PRK03983 | exosome complex exonuclease Rrp41; Provisional |
304-542 | 2.43e-23 | |||||||||||
exosome complex exonuclease Rrp41; Provisional Pssm-ID: 235187 [Multi-domain] Cd Length: 244 Bit Score: 99.71 E-value: 2.43e-23
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| Tex | COG2183 | Transcriptional accessory protein Tex/SPT6 [Transcription]; |
610-694 | 6.91e-23 | |||||||||||
Transcriptional accessory protein Tex/SPT6 [Transcription]; Pssm-ID: 441786 [Multi-domain] Cd Length: 719 Bit Score: 103.95 E-value: 6.91e-23
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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 ... |
623-691 | 3.93e-22 | |||||||||||
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: 90.42 E-value: 3.93e-22
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| rpsA | PRK06676 | 30S ribosomal protein S1; Reviewed |
560-691 | 4.53e-22 | |||||||||||
30S ribosomal protein S1; Reviewed Pssm-ID: 235851 [Multi-domain] Cd Length: 390 Bit Score: 98.79 E-value: 4.53e-22
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| RpsA | COG0539 | Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ... |
604-691 | 8.46e-22 | |||||||||||
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: 97.42 E-value: 8.46e-22
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| RNase_PH | cd11358 | RNase PH-like 3'-5' exoribonucleases; RNase PH-like 3'-5' exoribonucleases are enzymes that ... |
321-531 | 1.60e-21 | |||||||||||
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: 93.55 E-value: 1.60e-21
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| PRK00087 | PRK00087 | bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1; |
623-691 | 1.70e-21 | |||||||||||
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1; Pssm-ID: 234623 [Multi-domain] Cd Length: 647 Bit Score: 99.25 E-value: 1.70e-21
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| S1 | smart00316 | Ribosomal protein S1-like RNA-binding domain; |
621-691 | 4.81e-21 | |||||||||||
Ribosomal protein S1-like RNA-binding domain; Pssm-ID: 197648 [Multi-domain] Cd Length: 72 Bit Score: 87.27 E-value: 4.81e-21
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| RNase_PH_archRRP41 | cd11366 | RRP41 subunit of archaeal exosome; The RRP41 subunit of the archaeal exosome is a member of ... |
320-545 | 5.19e-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: 92.01 E-value: 5.19e-21
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| RpsA | COG0539 | Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ... |
615-691 | 1.70e-19 | |||||||||||
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: 90.49 E-value: 1.70e-19
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| rpsA | PRK06676 | 30S ribosomal protein S1; Reviewed |
616-691 | 5.67e-19 | |||||||||||
30S ribosomal protein S1; Reviewed Pssm-ID: 235851 [Multi-domain] Cd Length: 390 Bit Score: 89.55 E-value: 5.67e-19
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| rpsA | PRK13806 | 30S ribosomal protein S1; Provisional |
604-691 | 1.41e-18 | |||||||||||
30S ribosomal protein S1; Provisional Pssm-ID: 237516 [Multi-domain] Cd Length: 491 Bit Score: 89.40 E-value: 1.41e-18
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| PRK05807 | PRK05807 | RNA-binding protein S1; |
620-691 | 1.94e-18 | |||||||||||
RNA-binding protein S1; Pssm-ID: 235614 [Multi-domain] Cd Length: 136 Bit Score: 82.10 E-value: 1.94e-18
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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 ... |
623-691 | 1.19e-17 | |||||||||||
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: 78.05 E-value: 1.19e-17
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| rpsA | PRK06299 | 30S ribosomal protein S1; Reviewed |
560-690 | 1.40e-17 | |||||||||||
30S ribosomal protein S1; Reviewed Pssm-ID: 235775 [Multi-domain] Cd Length: 565 Bit Score: 86.76 E-value: 1.40e-17
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| PRK08582 | PRK08582 | RNA-binding protein S1; |
620-691 | 2.30e-17 | |||||||||||
RNA-binding protein S1; Pssm-ID: 236305 [Multi-domain] Cd Length: 139 Bit Score: 79.31 E-value: 2.30e-17
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| S1_Tex | cd05685 | S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has ... |
623-689 | 2.34e-17 | |||||||||||
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: 76.50 E-value: 2.34e-17
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| S1_dom_CvfD | NF040579 | CvfD/Ygs/GSP13 family RNA-binding post-transcriptional regulator; CvfD, Ygs, and GSP13 form a ... |
620-691 | 2.44e-17 | |||||||||||
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: 78.24 E-value: 2.44e-17
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| rpsA | PRK13806 | 30S ribosomal protein S1; Provisional |
615-691 | 9.33e-17 | |||||||||||
30S ribosomal protein S1; Provisional Pssm-ID: 237516 [Multi-domain] Cd Length: 491 Bit Score: 83.62 E-value: 9.33e-17
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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 ... |
622-689 | 1.05e-16 | |||||||||||
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: 74.97 E-value: 1.05e-16
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| S1 | pfam00575 | S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ... |
621-690 | 2.13e-16 | |||||||||||
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: 74.25 E-value: 2.13e-16
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| PRK08059 | PRK08059 | general stress protein 13; Validated |
620-691 | 1.29e-15 | |||||||||||
general stress protein 13; Validated Pssm-ID: 181215 [Multi-domain] Cd Length: 123 Bit Score: 73.54 E-value: 1.29e-15
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| S1_like | cd00164 | S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ... |
626-689 | 2.41e-15 | |||||||||||
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: 70.87 E-value: 2.41e-15
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| PRK00087 | PRK00087 | bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1; |
574-691 | 4.03e-15 | |||||||||||
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1; Pssm-ID: 234623 [Multi-domain] Cd Length: 647 Bit Score: 79.22 E-value: 4.03e-15
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| S1_IF2_alpha | cd04452 | S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain. ... |
621-691 | 2.22e-14 | |||||||||||
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: 68.38 E-value: 2.22e-14
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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 ... |
623-692 | 1.35e-13 | |||||||||||
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: 66.20 E-value: 1.35e-13
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| rpsA | PRK07899 | 30S ribosomal protein S1; Reviewed |
622-691 | 5.41e-13 | |||||||||||
30S ribosomal protein S1; Reviewed Pssm-ID: 236126 [Multi-domain] Cd Length: 486 Bit Score: 71.61 E-value: 5.41e-13
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| rpsA | PRK06299 | 30S ribosomal protein S1; Reviewed |
562-697 | 2.17e-12 | |||||||||||
30S ribosomal protein S1; Reviewed Pssm-ID: 235775 [Multi-domain] Cd Length: 565 Bit Score: 70.19 E-value: 2.17e-12
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| rpsA | TIGR00717 | ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ... |
560-691 | 4.15e-12 | |||||||||||
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: 68.99 E-value: 4.15e-12
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| RNase_PH_RRP41 | cd11370 | RRP41 subunit of eukaryotic exosome; The RRP41 subunit of eukaryotic exosome is a member of ... |
312-540 | 5.19e-12 | |||||||||||
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: 66.03 E-value: 5.19e-12
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| rpsA | PRK07899 | 30S ribosomal protein S1; Reviewed |
604-691 | 1.04e-11 | |||||||||||
30S ribosomal protein S1; Reviewed Pssm-ID: 236126 [Multi-domain] Cd Length: 486 Bit Score: 67.76 E-value: 1.04e-11
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| S1_RpoE | cd04460 | S1_RpoE: RpoE, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide ... |
624-691 | 1.07e-11 | |||||||||||
S1_RpoE: RpoE, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. RpoE is subunit E of archaeal RNA polymerase. Archaeal cells contain a single RNA polymerase made up of 12 subunits, which are homologous to the 12 subunits (RPB1-12) of eukaryotic RNA polymerase II. RpoE is homologous to Rpa43 of eukaryotic RNA polymerase I, RPB7 of eukaryotic RNA polymerase II, and Rpc25 of eukaryotic RNA polymerase III. RpoE is composed of two domains, the N-terminal RNP (ribonucleoprotein) domain and the C-terminal S1 domain. This S1 domain binds ssRNA and ssDNA. This family is classified based on the C-terminal S1 domain. The function of RpoE is not fully understood. In eukaryotes, RPB7 and RPB4 form a heterodimer that reversibly associates with the RNA polymerase II core. Pssm-ID: 239907 [Multi-domain] Cd Length: 99 Bit Score: 61.53 E-value: 1.07e-11
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| PRK03987 | PRK03987 | translation initiation factor IF-2 subunit alpha; Validated |
621-691 | 2.55e-11 | |||||||||||
translation initiation factor IF-2 subunit alpha; Validated Pssm-ID: 235188 [Multi-domain] Cd Length: 262 Bit Score: 64.46 E-value: 2.55e-11
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| S1_pNO40 | cd05686 | S1_pNO40: pNO40 , S1-like RNA-binding domain. pNO40 is a nucleolar protein of unknown function ... |
624-690 | 2.69e-11 | |||||||||||
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: 59.80 E-value: 2.69e-11
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| KH | smart00322 | K homology RNA-binding domain; |
553-617 | 3.07e-11 | |||||||||||
K homology RNA-binding domain; Pssm-ID: 197652 [Multi-domain] Cd Length: 68 Bit Score: 59.23 E-value: 3.07e-11
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| SUI2 | COG1093 | Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure ... |
621-691 | 3.36e-11 | |||||||||||
Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]; Translation initiation factor 2, alpha subunit (eIF-2alpha) is part of the Pathway/BioSystem: Translation factors Pssm-ID: 440710 [Multi-domain] Cd Length: 259 Bit Score: 64.06 E-value: 3.36e-11
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| PNPase | pfam03726 | Polyribonucleotide nucleotidyltransferase, RNA binding domain; This family contains the RNA ... |
251-317 | 8.10e-11 | |||||||||||
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: 58.45 E-value: 8.10e-11
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| KH_1 | pfam00013 | KH domain; KH motifs bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause ... |
556-615 | 3.17e-10 | |||||||||||
KH domain; KH motifs bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause paraneoplastic opsoclonus ataxia. Pssm-ID: 459630 [Multi-domain] Cd Length: 65 Bit Score: 56.52 E-value: 3.17e-10
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| PRK08563 | PRK08563 | DNA-directed RNA polymerase subunit E'; Provisional |
625-691 | 3.76e-10 | |||||||||||
DNA-directed RNA polymerase subunit E'; Provisional Pssm-ID: 236289 [Multi-domain] Cd Length: 187 Bit Score: 59.84 E-value: 3.76e-10
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| rpsA | PRK06299 | 30S ribosomal protein S1; Reviewed |
615-691 | 7.67e-10 | |||||||||||
30S ribosomal protein S1; Reviewed Pssm-ID: 235775 [Multi-domain] Cd Length: 565 Bit Score: 62.10 E-value: 7.67e-10
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| KH-I_DDX43_DDX53 | cd22430 | type I K homology (KH) RNA-binding domain found in DEAD box protein 43 (DDX43), DEAD box ... |
556-617 | 8.30e-10 | |||||||||||
type I K homology (KH) RNA-binding domain found in DEAD box protein 43 (DDX43), DEAD box protein 53 (DDX53) and similar proteins; DDX43 (also called cancer/testis antigen 13, or DEAD box protein HAGE, or helical antigen) displays tumor-specific expression. Diseases associated with DDX43 include rheumatoid lung disease. DDX53 (also called cancer-associated gene protein, or cancer/testis antigen 26, or DEAD box protein CAGE) shows high expression level in various tumors and is involved in anti-cancer drug resistance. Both DDX46 and DDX53 are members of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. Pssm-ID: 411858 [Multi-domain] Cd Length: 66 Bit Score: 55.37 E-value: 8.30e-10
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| S1_RNase_R | cd04471 | S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, ... |
623-690 | 2.53e-09 | |||||||||||
S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, which is a homolog of RNase II. RNase R degrades RNA with secondary structure having a 3' overhang of at least 7 nucleotides. RNase R and PNPase play an important role in the degradation of RNA with extensive secondary structure, such as rRNA, tRNA, and certain mRNA which contains repetitive extragenic palindromic sequences. The C-terminal S1 domain binds ssRNA. Pssm-ID: 239917 [Multi-domain] Cd Length: 83 Bit Score: 54.33 E-value: 2.53e-09
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| PRK00087 | PRK00087 | bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1; |
558-691 | 3.63e-09 | |||||||||||
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1; Pssm-ID: 234623 [Multi-domain] Cd Length: 647 Bit Score: 59.96 E-value: 3.63e-09
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| KH-I | cd00105 | K homology (KH) RNA-binding domain, type I; KH binds single-stranded RNA or DNA. It is found ... |
557-614 | 5.07e-09 | |||||||||||
K homology (KH) RNA-binding domain, type I; KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include an N-terminal extension and type I KH domains (e.g. hnRNP K) contain a C-terminal extension. Some KH-I superfamily members contain a divergent KH domain that lacks the RNA-binding GXXG motif. Some others have a mutated GXXG motif which may or may not have nucleic acid binding ability. Pssm-ID: 411802 [Multi-domain] Cd Length: 63 Bit Score: 52.69 E-value: 5.07e-09
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| VacB | COG0557 | Exoribonuclease R [Transcription]; |
623-690 | 8.97e-09 | |||||||||||
Exoribonuclease R [Transcription]; Pssm-ID: 440323 [Multi-domain] Cd Length: 711 Bit Score: 58.58 E-value: 8.97e-09
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| RNase_PH_C | pfam03725 | 3' exoribonuclease family, domain 2; This family includes 3'-5' exoribonucleases. Ribonuclease ... |
146-208 | 9.43e-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: 52.19 E-value: 9.43e-09
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| RNase_PH | cd11358 | RNase PH-like 3'-5' exoribonucleases; RNase PH-like 3'-5' exoribonucleases are enzymes that ... |
27-213 | 9.52e-09 | |||||||||||
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: 56.18 E-value: 9.52e-09
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| rpsA | TIGR00717 | ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ... |
616-691 | 1.76e-08 | |||||||||||
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: 57.44 E-value: 1.76e-08
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| KH-I_Vigilin_rpt6 | cd02394 | sixth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, ... |
554-618 | 2.74e-08 | |||||||||||
sixth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the sixth one. Pssm-ID: 411804 [Multi-domain] Cd Length: 68 Bit Score: 51.03 E-value: 2.74e-08
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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 ... |
623-682 | 4.60e-08 | |||||||||||
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: 50.18 E-value: 4.60e-08
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| PRK07252 | PRK07252 | S1 RNA-binding domain-containing protein; |
623-691 | 5.54e-08 | |||||||||||
S1 RNA-binding domain-containing protein; Pssm-ID: 180908 [Multi-domain] Cd Length: 120 Bit Score: 51.63 E-value: 5.54e-08
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| rpsA | TIGR00717 | ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ... |
623-691 | 5.60e-08 | |||||||||||
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: 55.90 E-value: 5.60e-08
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| KH-I_Dim2p_like_rpt1 | cd22389 | first type I K homology (KH) RNA-binding domain found in Pyrococcus horikoshii Dim2p and ... |
557-616 | 6.91e-08 | |||||||||||
first type I K homology (KH) RNA-binding domain found in Pyrococcus horikoshii Dim2p and similar proteins; The family includes a group of conserved KH domain-containing protein mainly from archaea, such as Dim2p homologues from Pyrococcus horikoshii and Aeropyrum pernix. Dim2p acts as a preribosomal RNA processing factor that has been identified as an essential protein for the maturation of 40S ribosomal subunit in Saccharomyces cerevisiae. It is required for the cleavage at processing site A2 to generate the pre-20S rRNA and for the dimethylation of the 18S rRNA by 18S rRNA dimethyltransferase, Dim1p. Dim2p contains two K-homology (KH) RNA-binding domains. The model corresponds to the first one. Pssm-ID: 411817 [Multi-domain] Cd Length: 70 Bit Score: 49.89 E-value: 6.91e-08
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| rpsA | TIGR00717 | ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ... |
572-691 | 2.16e-07 | |||||||||||
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: 53.97 E-value: 2.16e-07
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| KH-I_ScSCP160_rpt2 | cd22447 | second type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein ... |
553-618 | 3.03e-07 | |||||||||||
second type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein SCP160 and similar proteins; SCP160, also called protein HX, is a new yeast protein associated with the nuclear membrane and the endoplasmic reticulum. It is involved in the control of mitotic chromosome transmission. It is required during cell division for faithful partitioning of the ER-nuclear envelope membranes which enclose the duplicated chromosomes in yeast. SCP160 contains seven K-homology (KH) RNA-binding domains. The model corresponds to the second one. Pssm-ID: 411875 [Multi-domain] Cd Length: 80 Bit Score: 48.57 E-value: 3.03e-07
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| S1_Rrp5_repeat_hs5 | cd05697 | S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and ... |
623-688 | 3.67e-07 | |||||||||||
S1_Rrp5_repeat_hs5: 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 5 (hs5) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea. Pssm-ID: 240202 [Multi-domain] Cd Length: 69 Bit Score: 47.62 E-value: 3.67e-07
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| S1_RPS1_repeat_ec1_hs1 | cd05687 | S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ... |
623-691 | 4.35e-07 | |||||||||||
S1_RPS1_repeat_ec1_hs1: 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 1 of the Escherichia coli and Homo sapiens RPS1 (ec1 and hs1, respectively). Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog. Pssm-ID: 240192 [Multi-domain] Cd Length: 70 Bit Score: 47.52 E-value: 4.35e-07
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| Rrp42 | COG2123 | Exosome complex RNA-binding protein Rrp42, RNase PH superfamily [Intracellular trafficking, ... |
299-348 | 6.93e-07 | |||||||||||
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: 51.34 E-value: 6.93e-07
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| RNase_PH_RRP46 | cd11372 | RRP46 subunit of eukaryotic exosome; The RRP46 subunit of eukaryotic exosome is a member of ... |
321-469 | 7.24e-07 | |||||||||||
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: 50.26 E-value: 7.24e-07
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| rpsA | PRK06676 | 30S ribosomal protein S1; Reviewed |
613-680 | 7.35e-07 | |||||||||||
30S ribosomal protein S1; Reviewed Pssm-ID: 235851 [Multi-domain] Cd Length: 390 Bit Score: 52.18 E-value: 7.35e-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 ... |
617-689 | 1.24e-06 | |||||||||||
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: 46.45 E-value: 1.24e-06
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| KH-I_NOVA_rpt3 | cd09031 | third type I K homology (KH) RNA-binding domain found in the family of neuro-oncological ... |
557-614 | 1.86e-06 | |||||||||||
third type I K homology (KH) RNA-binding domain found in the family of neuro-oncological ventral antigen (Nova); The family includes two related neuronal RNA-binding proteins, Nova-1 and Nova-2. Nova-1, also called onconeural ventral antigen 1, or paraneoplastic Ri antigen, or ventral neuron-specific protein 1, may regulate RNA splicing or metabolism in a specific subset of developing neurons. It interacts with RNA containing repeats of the YCAY sequence. It is a brain-enriched splicing factor regulating neuronal alternative splicing. Nova-1 is involved in neurological disorders and carcinogenesis. Nova-2, also called astrocytic NOVA1-like RNA-binding protein, is a neuronal RNA-binding protein expressed in a broader central nervous system (CNS) distribution than Nova-1. It functions in neuronal RNA metabolism. NOVA family proteins contain three K-homology (KH) RNA-binding domains. The model corresponds to the third one. Pssm-ID: 411807 [Multi-domain] Cd Length: 71 Bit Score: 46.03 E-value: 1.86e-06
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| Krr1 | COG1094 | rRNA processing protein Krr1/Pno1, contains KH domain [Translation, ribosomal structure and ... |
559-616 | 2.01e-06 | |||||||||||
rRNA processing protein Krr1/Pno1, contains KH domain [Translation, ribosomal structure and biogenesis]; Pssm-ID: 440711 [Multi-domain] Cd Length: 177 Bit Score: 48.67 E-value: 2.01e-06
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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 ... |
610-690 | 2.08e-06 | |||||||||||
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: 46.04 E-value: 2.08e-06
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| PRK04282 | PRK04282 | exosome complex protein Rrp42; |
303-348 | 2.26e-06 | |||||||||||
exosome complex protein Rrp42; Pssm-ID: 235268 [Multi-domain] Cd Length: 271 Bit Score: 49.87 E-value: 2.26e-06
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| KH-I_ScSCP160_rpt1 | cd22446 | first type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein ... |
547-619 | 2.39e-06 | |||||||||||
first type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein SCP160 and similar proteins; SCP160, also called protein HX, is a new yeast protein associated with the nuclear membrane and the endoplasmic reticulum. It is involved in the control of mitotic chromosome transmission. It is required during cell division for faithful partitioning of the ER-nuclear envelope membranes which enclose the duplicated chromosomes in yeast. SCP160 contains seven K-homology (KH) RNA-binding domains. The model corresponds to the first one. Pssm-ID: 411874 [Multi-domain] Cd Length: 86 Bit Score: 45.86 E-value: 2.39e-06
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| KH_I_FMR1_FXR_rpt2 | cd22426 | second type I K homology (KH) RNA-binding domain found in a family of fragile X mental ... |
564-613 | 2.60e-06 | |||||||||||
second type I K homology (KH) RNA-binding domain found in a family of fragile X mental retardation protein (FMR1) and fragile X related (FXR) proteins; The FMR1/FXR family includes FMR1 (also known as FMRP) and its two homologues, fragile X related 1 (FXR1) and 2 (FXR2). They are involved in translational regulation, particularly in neuronal cells and play an important role in the regulation of glutamate-mediated neuronal activity and plasticity. Each of these three proteins can form heteromers with the others, and each can also form homomers. Lack of expression of FMR1 results in mental retardation and macroorchidism. FXR1 and FXR2 may play important roles in the function of FMR1 and in the pathogenesis of the Fragile X Mental Retardation Syndrome. Members of this family contain three K-homology (KH) RNA-binding domains. The model corresponds to the second one. Pssm-ID: 411854 [Multi-domain] Cd Length: 63 Bit Score: 45.21 E-value: 2.60e-06
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| arCOG04150 | TIGR03665 | arCOG04150 universal archaeal KH domain protein; This family of proteins is universal among ... |
559-616 | 2.82e-06 | |||||||||||
arCOG04150 universal archaeal KH domain protein; This family of proteins is universal among the 41 archaeal genomes analyzed, and is not observed outside of the archaea. The proteins contain a single KH domain (pfam00013) which is likely to confer the ability to bind RNA. Pssm-ID: 274711 [Multi-domain] Cd Length: 172 Bit Score: 47.94 E-value: 2.82e-06
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| RpsA | COG0539 | Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ... |
617-691 | 3.31e-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: 49.66 E-value: 3.31e-06
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| S1_RPS1_repeat_ec6 | cd05691 | S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ... |
623-694 | 6.18e-06 | |||||||||||
S1_RPS1_repeat_ec6: 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 6 (ec6) 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: 240196 [Multi-domain] Cd Length: 73 Bit Score: 44.57 E-value: 6.18e-06
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| PRK13763 | PRK13763 | putative RNA-processing protein; Provisional |
556-616 | 7.14e-06 | |||||||||||
putative RNA-processing protein; Provisional Pssm-ID: 237494 [Multi-domain] Cd Length: 180 Bit Score: 47.17 E-value: 7.14e-06
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| RNase_PH_archRRP42 | cd11365 | RRP42 subunit of archaeal exosome; The RRP42 subunit of the archaeal exosome is a member of ... |
306-348 | 8.11e-06 | |||||||||||
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: 47.98 E-value: 8.11e-06
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| PRK12269 | PRK12269 | bifunctional cytidylate kinase/ribosomal protein S1; Provisional |
614-691 | 9.00e-06 | |||||||||||
bifunctional cytidylate kinase/ribosomal protein S1; Provisional Pssm-ID: 105491 [Multi-domain] Cd Length: 863 Bit Score: 49.33 E-value: 9.00e-06
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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 ... |
623-685 | 9.77e-06 | |||||||||||
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: 43.72 E-value: 9.77e-06
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| KH-I_RNaseY | cd22431 | type I K homology (KH) RNA-binding domain found in ribonuclease Y (RNase Y) and similar ... |
558-627 | 1.30e-05 | |||||||||||
type I K homology (KH) RNA-binding domain found in ribonuclease Y (RNase Y) and similar proteins; RNase Y is an endoribonuclease that initiates mRNA decay. It initiates the decay of all SAM-dependent riboswitches, such as yitJ riboswitch. RNase Y is involved in processing of the gapA operon mRNA and it cleaves between cggR and gapA. It is also the decay-initiating endonuclease for rpsO mRNA. It plays a role in degradation of type I toxin-antitoxin system bsrG/SR4 RNAs and also a minor role in degradation of type I toxin-antitoxin system bsrE/SR5 degradation. Pssm-ID: 411859 [Multi-domain] Cd Length: 79 Bit Score: 43.72 E-value: 1.30e-05
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| KH-I_TDRKH_rpt1 | cd22428 | first type I K homology (KH) RNA-binding domain found in tudor and KH domain-containing ... |
556-617 | 1.72e-05 | |||||||||||
first type I K homology (KH) RNA-binding domain found in tudor and KH domain-containing protein (TDRKH) and similar proteins; TDRKH, also called tudor domain-containing protein 2 (TDRD2), is a mitochondria-anchored RNA-binding protein that is required for spermatogenesis and involved in piRNA biogenesis. It specifically recruits MIWI, but not MILI, to engage the piRNA pathway. TDRKH contains two K-homology (KH) RNA-binding domains and one tudor domain, which are involved in binding to RNA or single-strand DNA. The model corresponds to the first one. Pssm-ID: 411856 [Multi-domain] Cd Length: 74 Bit Score: 43.09 E-value: 1.72e-05
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| PRK09521 | PRK09521 | exosome complex RNA-binding protein Csl4; Provisional |
587-695 | 3.21e-05 | |||||||||||
exosome complex RNA-binding protein Csl4; Provisional Pssm-ID: 236547 [Multi-domain] Cd Length: 189 Bit Score: 45.35 E-value: 3.21e-05
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| RNase_PH_C | pfam03725 | 3' exoribonuclease family, domain 2; This family includes 3'-5' exoribonucleases. Ribonuclease ... |
458-529 | 3.48e-05 | |||||||||||
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: 42.18 E-value: 3.48e-05
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| PRK07400 | PRK07400 | 30S ribosomal protein S1; Reviewed |
617-691 | 5.03e-05 | |||||||||||
30S ribosomal protein S1; Reviewed Pssm-ID: 180960 [Multi-domain] Cd Length: 318 Bit Score: 45.95 E-value: 5.03e-05
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| S1_Rrp5_repeat_sc10 | cd05706 | S1_Rrp5_repeat_sc10: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ... |
620-691 | 7.94e-05 | |||||||||||
S1_Rrp5_repeat_sc10: 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 10 (sc10). Rrp5 is found in eukaryotes but not in prokaryotes or archaea. Pssm-ID: 240211 [Multi-domain] Cd Length: 73 Bit Score: 41.47 E-value: 7.94e-05
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| KH-I_FUBP_rpt1 | cd22396 | first type I K homology (KH) RNA-binding domain found in the FUBP family RNA/DNA-binding ... |
566-617 | 1.11e-04 | |||||||||||
first type I K homology (KH) RNA-binding domain found in the FUBP family RNA/DNA-binding proteins; The far upstream element-binding protein (FUBP) family includes FUBP1-3. FUBP1, also called FBP, or FUSE-binding protein 1, or DNA helicase V, or DH V, binds RNA and single-stranded DNA (ssDNA) and may act both as activator and repressor of transcription. It regulates MYC expression by binding to a single-stranded far-upstream element (FUSE) upstream of the MYC promoter. FUBP2, also called FUSE-binding protein 2, or KH type-splicing regulatory protein (KSRP), or p75, is a single-strand nucleic acid binding protein implicated in a variety of cellular processes, including splicing in the nucleus, mRNA decay, maturation of miRNA, and transcriptional control of proto-oncogenes such as c-myc. It regulates the stability and/or translatability of many mRNA species, encoding immune-relevant proteins, either by binding to AU-rich elements (AREs) of mRNA 3'UTR or by facilitating miRNA biogenesis to target mRNA. FUBP3, also called FUSE-binding protein 3, or MARTA2, was previously shown to mediate dendritic targeting of MAP2 mRNA in neurons. It may interact with single-stranded DNA from the far-upstream element (FUSE) and activate gene expression. It is required for beta-actin mRNA localization. It also interacts with fibroblast growth factor 9 (FGF9) 3'-UTR UG repeats and positively controls FGF9 expression through increasing translation of FGF9 mRNA. FUBP proteins contain four K-homology (KH) RNA-binding domains. The model corresponds to the first one. Pssm-ID: 411824 [Multi-domain] Cd Length: 68 Bit Score: 40.70 E-value: 1.11e-04
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| S1_Rrp5_repeat_sc11 | cd05707 | S1_Rrp5_repeat_sc11: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ... |
623-689 | 1.14e-04 | |||||||||||
S1_Rrp5_repeat_sc11: 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 11 (sc11). Rrp5 is found in eukaryotes but not in prokaryotes or archaea. Pssm-ID: 240212 [Multi-domain] Cd Length: 68 Bit Score: 40.74 E-value: 1.14e-04
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| KH-I_PEPPER_rpt2_like | cd22460 | second type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana RNA-binding KH ... |
559-615 | 1.83e-04 | |||||||||||
second type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana RNA-binding KH domain-containing protein PEPPER and similar proteins; The family includes a group of plant RNA-binding KH domain-containing proteins, such as PEPPER, flowering locus K homology domain protein (FLK), RNA-binding KH domain-containing protein RCF3 and KH domain-containing protein HEN4. PEPPER regulates vegetative and gynoecium development. It acts as a positive regulator of the central floral repressor FLOWERING LOCUS C. In concert with HUA2, PEPPER antagonizes FLK by positively regulating FLC probably at transcriptional and post-transcriptional levels, and thus acts as a negative regulator of flowering. FLK, also called flowering locus KH domain protein, regulates positively flowering by repressing FLC expression and post-transcriptional modification. PEPPER and FLK contain three K-homology (KH) RNA-binding domains. RCF3, also called protein ENHANCED STRESS RESPONSE 1 (ESR1), or protein HIGH OSMOTIC STRESS GENE EXPRESSION 5 (HOS5), or protein REGULATOR OF CBF GENE EXPRESSION 3, or protein SHINY 1 (SHI1), acts as negative regulator of osmotic stress-induced gene expression. It is involved in the regulation of thermotolerance responses under heat stress. It functions as an upstream regulator of heat stress transcription factor (HSF) genes. HEN4, also called protein HUA ENHANCER 4, plays a role in floral reproductive organ identity in the third whorl and floral determinacy specification by specifically promoting the processing of AGAMOUS (AG) pre-mRNA. It functions in association with HUA1 and HUA2. RCF3 and HEN4 contain five KH RNA-binding domains. The model corresponds to the KH2 domain of PEPPER and FLK, as well as KH2 and KH4 domains of RCF3 and HEN4. Pssm-ID: 411888 [Multi-domain] Cd Length: 73 Bit Score: 40.30 E-value: 1.83e-04
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| KH-I_IGF2BP_rpt1 | cd22400 | first type I K homology (KH) RNA-binding domain found in the insulin-like growth factor 2 ... |
563-617 | 1.97e-04 | |||||||||||
first type I K homology (KH) RNA-binding domain found in the insulin-like growth factor 2 mRNA-binding protein (IGF2BP) family; The IGF2BP family includes three members: IGF2BP1/IMP-1/ CRD-BP/ VICKZ1, IGF2BP2/IMP-2/ VICKZ2, and IGF2BP3/IMP-3/VICKZ3, which are RNA-binding factors that recruit target transcripts to cytoplasmic protein-RNA complexes (mRNPs). They function by binding to the 5' UTR of the insulin-like growth factor 2 (IGF2) mRNA and regulating IGF2 translation. IGF2BP proteins contain four K-homology (KH) RNA-binding domains which are important in RNA binding and are known to be involved in RNA synthesis and metabolism. The model corresponds to the first one. Pssm-ID: 411828 [Multi-domain] Cd Length: 68 Bit Score: 39.95 E-value: 1.97e-04
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| S1_Rrp5_repeat_hs13 | cd05704 | S1_Rrp5_repeat_hs13: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ... |
620-691 | 2.11e-04 | |||||||||||
S1_Rrp5_repeat_hs13: 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 13 (hs13). Rrp5 is found in eukaryotes but not in prokaryotes or archaea. Pssm-ID: 240209 [Multi-domain] Cd Length: 72 Bit Score: 40.03 E-value: 2.11e-04
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| KH-I_PCBP_rpt1 | cd22438 | first type I K homology (KH) RNA-binding domain found in the family of poly(C)-binding ... |
566-600 | 2.23e-04 | |||||||||||
first type I K homology (KH) RNA-binding domain found in the family of poly(C)-binding proteins (PCBPs); The PCBP family, also known as hnRNP E family, comprises four members, PCBP1-4, which are RNA-binding proteins that interact in a sequence-specific manner with single-stranded poly(C) sequences. They are mainly involved in various posttranscriptional regulations, including mRNA stabilization or translational activation/silencing. Besides, PCBPs may share iron chaperone activity. PCBPs contain three K-homology (KH) RNA-binding domains. The model corresponds to the first one. Pssm-ID: 411866 [Multi-domain] Cd Length: 67 Bit Score: 39.93 E-value: 2.23e-04
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| KH-I_ScSCP160_rpt4 | cd22449 | fourth type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein ... |
557-618 | 2.25e-04 | |||||||||||
fourth type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein SCP160 and similar proteins; SCP160, also called protein HX, is a new yeast protein associated with the nuclear membrane and the endoplasmic reticulum. It is involved in the control of mitotic chromosome transmission. It is required during cell division for faithful partitioning of the ER-nuclear envelope membranes which enclose the duplicated chromosomes in yeast. SCP160 contains seven K-homology (KH) RNA-binding domains. The model corresponds to the fourth one. Pssm-ID: 411877 [Multi-domain] Cd Length: 70 Bit Score: 39.95 E-value: 2.25e-04
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| KH-I_PEPPER_rpt1_like | cd22459 | first type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana RNA-binding KH ... |
563-593 | 3.13e-04 | |||||||||||
first type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana RNA-binding KH domain-containing protein PEPPER and similar proteins; The family includes a group of plant RNA-binding KH domain-containing proteins, such as PEPPER, flowering locus K homology domain protein (FLK), RNA-binding KH domain-containing protein RCF3 and KH domain-containing protein HEN4. PEPPER regulates vegetative and gynoecium development. It acts as a positive regulator of the central floral repressor FLOWERING LOCUS C. In concert with HUA2, PEPPER antagonizes FLK by positively regulating FLC probably at transcriptional and post-transcriptional levels, and thus acts as a negative regulator of flowering. FLK, also called flowering locus KH domain protein, regulates positively flowering by repressing FLC expression and post-transcriptional modification. PEPPER and FLK contain three K-homology (KH) RNA-binding domains. RCF3, also called protein ENHANCED STRESS RESPONSE 1 (ESR1), or protein HIGH OSMOTIC STRESS GENE EXPRESSION 5 (HOS5), or protein REGULATOR OF CBF GENE EXPRESSION 3, or protein SHINY 1 (SHI1), acts as negative regulator of osmotic stress-induced gene expression. It is involved in the regulation of thermotolerance responses under heat stress. It functions as an upstream regulator of heat stress transcription factor (HSF) genes. HEN4, also called protein HUA ENHANCER 4, plays a role in floral reproductive organ identity in the third whorl and floral determinacy specification by specifically promoting the processing of AGAMOUS (AG) pre-mRNA. It functions in association with HUA1 and HUA2. RCF3 and HEN4 contain five KH RNA-binding domains. The model corresponds to the KH1 domain of PEPPER and FLK, as well as KH1 and KH3 domains of RCF3 and HEN4. Pssm-ID: 411887 [Multi-domain] Cd Length: 69 Bit Score: 39.51 E-value: 3.13e-04
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| KH-I_Rrp4_prokar | cd22524 | type I K homology (KH) RNA-binding domain found in exosome complex component Rrp4 mainly from ... |
561-618 | 3.60e-04 | |||||||||||
type I K homology (KH) RNA-binding domain found in exosome complex component Rrp4 mainly from archaea; The subfamily corresponds to ribosomal RNA-processing protein 4 (Rrp4) mainly from archaea. It is a non-catalytic component of the exosome, which is a phosphorolytic 3'-5' exoribonuclease complex involved in RNA degradation and processing. Rrp4 increases the RNA binding and the efficiency of RNA degradation and confers strong poly(A) specificity to the exosome. Pssm-ID: 411952 [Multi-domain] Cd Length: 82 Bit Score: 39.88 E-value: 3.60e-04
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| PRK12269 | PRK12269 | bifunctional cytidylate kinase/ribosomal protein S1; Provisional |
607-691 | 3.63e-04 | |||||||||||
bifunctional cytidylate kinase/ribosomal protein S1; Provisional Pssm-ID: 105491 [Multi-domain] Cd Length: 863 Bit Score: 43.93 E-value: 3.63e-04
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| RNase_PH_RRP42 | cd11367 | RRP42 subunit of eukaryotic exosome; The RRP42 subunit of eukaryotic exosome is a member of ... |
312-348 | 3.88e-04 | |||||||||||
RRP42 subunit of eukaryotic exosome; The RRP42 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: 206772 [Multi-domain] Cd Length: 272 Bit Score: 42.97 E-value: 3.88e-04
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| rpsA | PRK06299 | 30S ribosomal protein S1; Reviewed |
618-689 | 1.10e-03 | |||||||||||
30S ribosomal protein S1; Reviewed Pssm-ID: 235775 [Multi-domain] Cd Length: 565 Bit Score: 42.07 E-value: 1.10e-03
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| RNase_PH_RRP43 | cd11369 | RRP43 subunit of eukaryotic exosome; The RRP43 subunit of eukaryotic exosome is a member of ... |
307-348 | 1.48e-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: 41.00 E-value: 1.48e-03
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| rpsA | PRK13806 | 30S ribosomal protein S1; Provisional |
622-697 | 1.64e-03 | |||||||||||
30S ribosomal protein S1; Provisional Pssm-ID: 237516 [Multi-domain] Cd Length: 491 Bit Score: 41.63 E-value: 1.64e-03
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| KH-I_TDRKH_rpt2 | cd22429 | second type I K homology (KH) RNA-binding domain found in tudor and KH domain-containing ... |
566-621 | 1.84e-03 | |||||||||||
second type I K homology (KH) RNA-binding domain found in tudor and KH domain-containing protein (TDRKH) and similar proteins; TDRKH, also called tudor domain-containing protein 2 (TDRD2), is a mitochondria-anchored RNA-binding protein that is required for spermatogenesis and involved in piRNA biogenesis. It specifically recruits MIWI, but not MILI, to engage the piRNA pathway. TDRKH contains two K-homology (KH) RNA-binding domains and one tudor domain, which are involved in binding to RNA or single-strand DNA. The model corresponds to the second one. Pssm-ID: 411857 [Multi-domain] Cd Length: 82 Bit Score: 37.70 E-value: 1.84e-03
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| KH-I_Vigilin_rpt8 | cd22411 | eighth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; ... |
557-614 | 2.32e-03 | |||||||||||
eighth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the eighth one. Pssm-ID: 411839 [Multi-domain] Cd Length: 62 Bit Score: 36.80 E-value: 2.32e-03
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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 ... |
623-691 | 2.76e-03 | |||||||||||
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: 36.82 E-value: 2.76e-03
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| KH-I_FUBP_rpt4 | cd22399 | fourth type I K homology (KH) RNA-binding domain found in the FUBP family RNA/DNA-binding ... |
557-593 | 3.58e-03 | |||||||||||
fourth type I K homology (KH) RNA-binding domain found in the FUBP family RNA/DNA-binding proteins; The far upstream element-binding protein (FUBP) family includes FUBP1-3. FUBP1, also called FBP, or FUSE-binding protein 1, or DNA helicase V, or DH V, binds RNA and single-stranded DNA (ssDNA) and may act both as activator and repressor of transcription. It regulates MYC expression by binding to a single-stranded far-upstream element (FUSE) upstream of the MYC promoter. FUBP2, also called FUSE-binding protein 2, or KH type-splicing regulatory protein (KSRP), or p75, is a single-strand nucleic acid binding protein implicated in a variety of cellular processes, including splicing in the nucleus, mRNA decay, maturation of miRNA, and transcriptional control of proto-oncogenes such as c-myc. It regulates the stability and/or translatability of many mRNA species, encoding immune-relevant proteins, either by binding to AU-rich elements (AREs) of mRNA 3'UTR or by facilitating miRNA biogenesis to target mRNA. FUBP3, also called FUSE-binding protein 3, or MARTA2, was previously shown to mediate dendritic targeting of MAP2 mRNA in neurons. It may interact with single-stranded DNA from the far-upstream element (FUSE) and activate gene expression. It is required for beta-actin mRNA localization. It also interacts with fibroblast growth factor 9 (FGF9) 3'-UTR UG repeats and positively controls FGF9 expression through increasing translation of FGF9 mRNA. FUBP proteins contain four K-homology (KH) RNA-binding domains. The model corresponds to the fourth one. Pssm-ID: 411827 [Multi-domain] Cd Length: 67 Bit Score: 36.43 E-value: 3.58e-03
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| KH_4 | pfam13083 | KH domain; |
555-580 | 3.81e-03 | |||||||||||
KH domain; Pssm-ID: 463779 Cd Length: 73 Bit Score: 36.69 E-value: 3.81e-03
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| KH-I_FUBP3_rpt4 | cd22489 | fourth type I K homology (KH) RNA-binding domain found in far upstream element-binding protein ... |
557-593 | 4.49e-03 | |||||||||||
fourth type I K homology (KH) RNA-binding domain found in far upstream element-binding protein 3 (FUBP3) and similar proteins; FUBP3, also called FUSE-binding protein 3, or MARTA2, was previously shown to mediate dendritic targeting of MAP2 mRNA in neurons. It may interact with single-stranded DNA from the far-upstream element (FUSE) and activate gene expression. It is required for beta-actin mRNA localization. It also interacts with fibroblast growth factor 9 (FGF9) 3'-UTR UG repeats and positively controls FGF9 expression through increasing translation of FGF9 mRNA. FUBP3 contains four K-homology (KH) RNA-binding domains. The model corresponds to the fourth one. Pssm-ID: 411917 [Multi-domain] Cd Length: 69 Bit Score: 36.45 E-value: 4.49e-03
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| PTZ00248 | PTZ00248 | eukaryotic translation initiation factor 2 subunit 1; Provisional |
621-691 | 5.08e-03 | |||||||||||
eukaryotic translation initiation factor 2 subunit 1; Provisional Pssm-ID: 240329 [Multi-domain] Cd Length: 319 Bit Score: 39.65 E-value: 5.08e-03
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| PRK04163 | PRK04163 | exosome complex protein Rrp4; |
561-616 | 5.55e-03 | |||||||||||
exosome complex protein Rrp4; Pssm-ID: 235233 [Multi-domain] Cd Length: 235 Bit Score: 39.10 E-value: 5.55e-03
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| KH-I_HNRNPK_rpt3 | cd22434 | third type I K homology (KH) RNA-binding domain found in heterogeneous nuclear ... |
561-600 | 8.00e-03 | |||||||||||
third type I K homology (KH) RNA-binding domain found in heterogeneous nuclear ribonucleoprotein K (hnRNP K) and similar proteins; hnRNP K, also called transformation up-regulated nuclear protein (TUNP), is a pre-mRNA binding protein that binds tenaciously to poly(C) sequences. It may be involved in the nuclear metabolism of hnRNAs, particularly for pre-mRNAs that contain cytidine-rich sequences. It can also bind poly(C) single-stranded DNA. hnRNP K plays an important role in p53/TP53 response to DNA damage, acting at the level of both transcription activation and repression. hnRNP K contains three K-homology (KH) RNA-binding domains. The model corresponds to the third one. Pssm-ID: 411862 [Multi-domain] Cd Length: 74 Bit Score: 35.76 E-value: 8.00e-03
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