3'-to-5' exoribonuclease RNase R [Staphylococcus aureus]
Protein Classification
ribonuclease R( domain architecture ID 11493488)
ribonuclease R is a 3' to 5' hydrolytic exoribonuclease able to digest highly structured RNA
List of domain hits
| Name | Accession | Description | Interval | E-value | ||||||||||
| RNase_R | TIGR02063 | ribonuclease R; This family consists of an exoribonuclease, ribonuclease R, also called VacB. ... |
1-711 | 0e+00 | ||||||||||
ribonuclease R; This family consists of an exoribonuclease, ribonuclease R, also called VacB. It is one of the eight exoribonucleases reported in E. coli and is broadly distributed throughout the bacteria. In E. coli, double mutants of this protein and polynucleotide phosphorylase are not viable. Scoring between trusted and noise cutoffs to the model are shorter, divergent forms from the Chlamydiae, and divergent forms from the Campylobacterales (including Helicobacter pylori) and Leptospira interrogans. [Transcription, Degradation of RNA] : Pssm-ID: 273947 [Multi-domain] Cd Length: 709 Bit Score: 1044.93 E-value: 0e+00
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| Name | Accession | Description | Interval | E-value | |||||||||||
| RNase_R | TIGR02063 | ribonuclease R; This family consists of an exoribonuclease, ribonuclease R, also called VacB. ... |
1-711 | 0e+00 | |||||||||||
ribonuclease R; This family consists of an exoribonuclease, ribonuclease R, also called VacB. It is one of the eight exoribonucleases reported in E. coli and is broadly distributed throughout the bacteria. In E. coli, double mutants of this protein and polynucleotide phosphorylase are not viable. Scoring between trusted and noise cutoffs to the model are shorter, divergent forms from the Chlamydiae, and divergent forms from the Campylobacterales (including Helicobacter pylori) and Leptospira interrogans. [Transcription, Degradation of RNA] Pssm-ID: 273947 [Multi-domain] Cd Length: 709 Bit Score: 1044.93 E-value: 0e+00
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| VacB | COG0557 | Exoribonuclease R [Transcription]; |
2-717 | 0e+00 | |||||||||||
Exoribonuclease R [Transcription]; Pssm-ID: 440323 [Multi-domain] Cd Length: 711 Bit Score: 1037.37 E-value: 0e+00
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| PRK11642 | PRK11642 | ribonuclease R; |
18-745 | 9.19e-155 | |||||||||||
ribonuclease R; Pssm-ID: 236944 [Multi-domain] Cd Length: 813 Bit Score: 471.15 E-value: 9.19e-155
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| RNB | pfam00773 | RNB domain; This domain is the catalytic domain of ribonuclease II. |
251-579 | 1.16e-132 | |||||||||||
RNB domain; This domain is the catalytic domain of ribonuclease II. Pssm-ID: 459934 [Multi-domain] Cd Length: 314 Bit Score: 396.65 E-value: 1.16e-132
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| RNB | smart00955 | This domain is the catalytic domain of ribonuclease II; |
251-581 | 1.24e-123 | |||||||||||
This domain is the catalytic domain of ribonuclease II; Pssm-ID: 214935 [Multi-domain] Cd Length: 286 Bit Score: 371.99 E-value: 1.24e-123
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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, ... |
630-711 | 1.82e-36 | |||||||||||
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: 131.75 E-value: 1.82e-36
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| Name | Accession | Description | Interval | E-value | |||||||||||
| RNase_R | TIGR02063 | ribonuclease R; This family consists of an exoribonuclease, ribonuclease R, also called VacB. ... |
1-711 | 0e+00 | |||||||||||
ribonuclease R; This family consists of an exoribonuclease, ribonuclease R, also called VacB. It is one of the eight exoribonucleases reported in E. coli and is broadly distributed throughout the bacteria. In E. coli, double mutants of this protein and polynucleotide phosphorylase are not viable. Scoring between trusted and noise cutoffs to the model are shorter, divergent forms from the Chlamydiae, and divergent forms from the Campylobacterales (including Helicobacter pylori) and Leptospira interrogans. [Transcription, Degradation of RNA] Pssm-ID: 273947 [Multi-domain] Cd Length: 709 Bit Score: 1044.93 E-value: 0e+00
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| VacB | COG0557 | Exoribonuclease R [Transcription]; |
2-717 | 0e+00 | |||||||||||
Exoribonuclease R [Transcription]; Pssm-ID: 440323 [Multi-domain] Cd Length: 711 Bit Score: 1037.37 E-value: 0e+00
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| 3_prime_RNase | TIGR00358 | VacB and RNase II family 3'-5' exoribonucleases; This model is defined to identify a pair of ... |
61-711 | 0e+00 | |||||||||||
VacB and RNase II family 3'-5' exoribonucleases; This model is defined to identify a pair of paralogous 3-prime exoribonucleases in E. coli, plus the set of proteins apparently orthologous to one or the other in other eubacteria. VacB was characterized originally as required for the expression of virulence genes, but is now recognized as the exoribonuclease RNase R (Rnr). Its paralog in E. coli and H. influenzae is designated exoribonuclease II (Rnb). Both are involved in the degradation of mRNA, and consequently have strong pleiotropic effects that may be difficult to disentangle. Both these proteins share domain-level similarity (RNB, S1) with a considerable number of other proteins, and full-length similarity scoring below the trusted cutoff to proteins associated with various phenotypes but uncertain biochemistry; it may be that these latter proteins are also 3-prime exoribonucleases. [Transcription, Degradation of RNA] Pssm-ID: 273033 [Multi-domain] Cd Length: 654 Bit Score: 680.28 E-value: 0e+00
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| PRK11642 | PRK11642 | ribonuclease R; |
18-745 | 9.19e-155 | |||||||||||
ribonuclease R; Pssm-ID: 236944 [Multi-domain] Cd Length: 813 Bit Score: 471.15 E-value: 9.19e-155
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| RNB | pfam00773 | RNB domain; This domain is the catalytic domain of ribonuclease II. |
251-579 | 1.16e-132 | |||||||||||
RNB domain; This domain is the catalytic domain of ribonuclease II. Pssm-ID: 459934 [Multi-domain] Cd Length: 314 Bit Score: 396.65 E-value: 1.16e-132
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| RNB | smart00955 | This domain is the catalytic domain of ribonuclease II; |
251-581 | 1.24e-123 | |||||||||||
This domain is the catalytic domain of ribonuclease II; Pssm-ID: 214935 [Multi-domain] Cd Length: 286 Bit Score: 371.99 E-value: 1.24e-123
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| Rnb | COG4776 | Exoribonuclease II [Transcription]; |
61-715 | 5.48e-67 | |||||||||||
Exoribonuclease II [Transcription]; Pssm-ID: 443808 [Multi-domain] Cd Length: 644 Bit Score: 234.36 E-value: 5.48e-67
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| PRK05054 | PRK05054 | exoribonuclease II; Provisional |
72-715 | 6.37e-52 | |||||||||||
exoribonuclease II; Provisional Pssm-ID: 179920 [Multi-domain] Cd Length: 644 Bit Score: 192.01 E-value: 6.37e-52
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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, ... |
630-711 | 1.82e-36 | |||||||||||
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: 131.75 E-value: 1.82e-36
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| CSD2 | pfam17876 | Cold shock domain; Crystallographic structure analysis of E. coli wild-type RNase II revealed ... |
155-229 | 1.52e-32 | |||||||||||
Cold shock domain; Crystallographic structure analysis of E. coli wild-type RNase II revealed that the amino-terminal region starts with an alpha-helix followed by two consecutive five-stranded anti-parallel beta-barrels, identified as cold-shock domains (CSD1 and CSD2). This entry relates to CSD2 which lacks the typical sequence motifs RNPI and RNPII but contributes to RNA binding. Pssm-ID: 465546 [Multi-domain] Cd Length: 74 Bit Score: 120.19 E-value: 1.52e-32
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| OB_RNB | pfam08206 | Ribonuclease B OB domain; This family includes the N-terminal OB domain found in ribonuclease ... |
75-135 | 8.85e-15 | |||||||||||
Ribonuclease B OB domain; This family includes the N-terminal OB domain found in ribonuclease B proteins in one or two copies. Pssm-ID: 429863 [Multi-domain] Cd Length: 58 Bit Score: 69.10 E-value: 8.85e-15
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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 ... |
635-704 | 4.19e-13 | |||||||||||
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: 65.77 E-value: 4.19e-13
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| S1 | smart00316 | Ribosomal protein S1-like RNA-binding domain; |
630-708 | 9.74e-13 | |||||||||||
Ribosomal protein S1-like RNA-binding domain; Pssm-ID: 197648 [Multi-domain] Cd Length: 72 Bit Score: 63.78 E-value: 9.74e-13
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| PRK08563 | PRK08563 | DNA-directed RNA polymerase subunit E'; Provisional |
635-704 | 2.01e-12 | |||||||||||
DNA-directed RNA polymerase subunit E'; Provisional Pssm-ID: 236289 [Multi-domain] Cd Length: 187 Bit Score: 66.39 E-value: 2.01e-12
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| S1 | pfam00575 | S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ... |
630-710 | 2.07e-12 | |||||||||||
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: 63.08 E-value: 2.07e-12
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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 ... |
631-705 | 3.04e-10 | |||||||||||
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: 56.52 E-value: 3.04e-10
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| PRK11824 | PRK11824 | polynucleotide phosphorylase/polyadenylase; Provisional |
616-704 | 1.20e-09 | |||||||||||
polynucleotide phosphorylase/polyadenylase; Provisional Pssm-ID: 236995 [Multi-domain] Cd Length: 693 Bit Score: 61.60 E-value: 1.20e-09
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| S1_like | cd00164 | S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ... |
634-706 | 4.41e-09 | |||||||||||
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: 53.15 E-value: 4.41e-09
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| OB_RNB | pfam08206 | Ribonuclease B OB domain; This family includes the N-terminal OB domain found in ribonuclease ... |
153-201 | 9.60e-09 | |||||||||||
Ribonuclease B OB domain; This family includes the N-terminal OB domain found in ribonuclease B proteins in one or two copies. Pssm-ID: 429863 [Multi-domain] Cd Length: 58 Bit Score: 52.16 E-value: 9.60e-09
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| RpsA | COG0539 | Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ... |
608-700 | 1.63e-08 | |||||||||||
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: 57.36 E-value: 1.63e-08
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| rpsA | PRK06299 | 30S ribosomal protein S1; Reviewed |
630-706 | 2.10e-08 | |||||||||||
30S ribosomal protein S1; Reviewed Pssm-ID: 235775 [Multi-domain] Cd Length: 565 Bit Score: 57.48 E-value: 2.10e-08
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| S1_Tex | cd05685 | S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has ... |
631-706 | 2.16e-08 | |||||||||||
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: 51.46 E-value: 2.16e-08
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| YabR | COG1098 | Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function ... |
630-741 | 3.68e-08 | |||||||||||
Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function prediction only]; Pssm-ID: 440715 [Multi-domain] Cd Length: 130 Bit Score: 52.49 E-value: 3.68e-08
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| RpsA | COG0539 | Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ... |
629-706 | 6.51e-08 | |||||||||||
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: 55.44 E-value: 6.51e-08
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| S1_PNPase | cd04472 | S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a ... |
631-705 | 9.52e-08 | |||||||||||
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: 49.46 E-value: 9.52e-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 ... |
631-705 | 1.98e-07 | |||||||||||
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: 48.64 E-value: 1.98e-07
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| S1_RPS1_repeat_ec3 | cd05688 | S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ... |
630-706 | 2.16e-07 | |||||||||||
S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 3 (ec3) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog. Pssm-ID: 240193 [Multi-domain] Cd Length: 68 Bit Score: 48.39 E-value: 2.16e-07
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| rpsA | PRK06676 | 30S ribosomal protein S1; Reviewed |
629-706 | 3.40e-07 | |||||||||||
30S ribosomal protein S1; Reviewed Pssm-ID: 235851 [Multi-domain] Cd Length: 390 Bit Score: 53.34 E-value: 3.40e-07
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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 ... |
629-708 | 1.15e-06 | |||||||||||
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: 46.94 E-value: 1.15e-06
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| rpsA | PRK06299 | 30S ribosomal protein S1; Reviewed |
631-706 | 1.18e-06 | |||||||||||
30S ribosomal protein S1; Reviewed Pssm-ID: 235775 [Multi-domain] Cd Length: 565 Bit Score: 52.09 E-value: 1.18e-06
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| CSP | smart00357 | Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ... |
74-135 | 1.31e-06 | |||||||||||
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria and is involved in regulating translation in eukaryotes. Contains sub-family of RNA-binding domains in the Rho transcription termination factor. Pssm-ID: 214633 [Multi-domain] Cd Length: 64 Bit Score: 46.05 E-value: 1.31e-06
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| rpsA | TIGR00717 | ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ... |
631-710 | 1.55e-06 | |||||||||||
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: 51.66 E-value: 1.55e-06
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| rpsA | PRK06299 | 30S ribosomal protein S1; Reviewed |
608-702 | 2.06e-06 | |||||||||||
30S ribosomal protein S1; Reviewed Pssm-ID: 235775 [Multi-domain] Cd Length: 565 Bit Score: 51.32 E-value: 2.06e-06
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| PRK00087 | PRK00087 | bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1; |
629-706 | 2.75e-06 | |||||||||||
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1; Pssm-ID: 234623 [Multi-domain] Cd Length: 647 Bit Score: 50.72 E-value: 2.75e-06
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| rpsA | PRK13806 | 30S ribosomal protein S1; Provisional |
631-706 | 2.78e-06 | |||||||||||
30S ribosomal protein S1; Provisional Pssm-ID: 237516 [Multi-domain] Cd Length: 491 Bit Score: 50.49 E-value: 2.78e-06
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| PRK08582 | PRK08582 | RNA-binding protein S1; |
626-744 | 4.37e-06 | |||||||||||
RNA-binding protein S1; Pssm-ID: 236305 [Multi-domain] Cd Length: 139 Bit Score: 46.95 E-value: 4.37e-06
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| Tex | COG2183 | Transcriptional accessory protein Tex/SPT6 [Transcription]; |
618-702 | 1.44e-05 | |||||||||||
Transcriptional accessory protein Tex/SPT6 [Transcription]; Pssm-ID: 441786 [Multi-domain] Cd Length: 719 Bit Score: 48.48 E-value: 1.44e-05
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| rpsA | TIGR00717 | ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ... |
631-706 | 1.91e-05 | |||||||||||
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found in most bacterial genomes in a single copy, but is not present in the Mycoplasmas. It is heterogeneous with respect to the number of repeats of the S1 RNA binding domain described by pfam00575: six repeats in E. coli and most other bacteria, four in Bacillus subtilis and some other species. rpsA is an essential gene in E. coli but not in B. subtilis. It is associated with the cytidylate kinase gene cmk in many species, and fused to it in Treponema pallidum. RpsA is proposed (Medline:97323001) to assist in mRNA degradation. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned. [Protein synthesis, Ribosomal proteins: synthesis and modification] Pssm-ID: 273232 [Multi-domain] Cd Length: 516 Bit Score: 48.19 E-value: 1.91e-05
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| rpsA | PRK13806 | 30S ribosomal protein S1; Provisional |
608-704 | 2.17e-05 | |||||||||||
30S ribosomal protein S1; Provisional Pssm-ID: 237516 [Multi-domain] Cd Length: 491 Bit Score: 47.80 E-value: 2.17e-05
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| rpsA | TIGR00717 | ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ... |
608-706 | 5.47e-05 | |||||||||||
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found in most bacterial genomes in a single copy, but is not present in the Mycoplasmas. It is heterogeneous with respect to the number of repeats of the S1 RNA binding domain described by pfam00575: six repeats in E. coli and most other bacteria, four in Bacillus subtilis and some other species. rpsA is an essential gene in E. coli but not in B. subtilis. It is associated with the cytidylate kinase gene cmk in many species, and fused to it in Treponema pallidum. RpsA is proposed (Medline:97323001) to assist in mRNA degradation. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned. [Protein synthesis, Ribosomal proteins: synthesis and modification] Pssm-ID: 273232 [Multi-domain] Cd Length: 516 Bit Score: 46.65 E-value: 5.47e-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 ... |
630-706 | 9.13e-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: 9.13e-05
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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 ... |
631-706 | 2.20e-04 | |||||||||||
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: 40.25 E-value: 2.20e-04
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| rpsA | PRK06676 | 30S ribosomal protein S1; Reviewed |
608-710 | 2.22e-04 | |||||||||||
30S ribosomal protein S1; Reviewed Pssm-ID: 235851 [Multi-domain] Cd Length: 390 Bit Score: 44.48 E-value: 2.22e-04
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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 ... |
634-699 | 2.74e-04 | |||||||||||
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: 40.30 E-value: 2.74e-04
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| rpsA | PRK06299 | 30S ribosomal protein S1; Reviewed |
629-706 | 2.89e-04 | |||||||||||
30S ribosomal protein S1; Reviewed Pssm-ID: 235775 [Multi-domain] Cd Length: 565 Bit Score: 44.38 E-value: 2.89e-04
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| rpsA | PRK07899 | 30S ribosomal protein S1; Reviewed |
630-706 | 3.85e-04 | |||||||||||
30S ribosomal protein S1; Reviewed Pssm-ID: 236126 [Multi-domain] Cd Length: 486 Bit Score: 43.88 E-value: 3.85e-04
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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 ... |
631-706 | 4.38e-04 | |||||||||||
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: 39.14 E-value: 4.38e-04
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| rpsA | TIGR00717 | ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ... |
630-733 | 5.44e-04 | |||||||||||
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found in most bacterial genomes in a single copy, but is not present in the Mycoplasmas. It is heterogeneous with respect to the number of repeats of the S1 RNA binding domain described by pfam00575: six repeats in E. coli and most other bacteria, four in Bacillus subtilis and some other species. rpsA is an essential gene in E. coli but not in B. subtilis. It is associated with the cytidylate kinase gene cmk in many species, and fused to it in Treponema pallidum. RpsA is proposed (Medline:97323001) to assist in mRNA degradation. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned. [Protein synthesis, Ribosomal proteins: synthesis and modification] Pssm-ID: 273232 [Multi-domain] Cd Length: 516 Bit Score: 43.18 E-value: 5.44e-04
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| PRK12269 | PRK12269 | bifunctional cytidylate kinase/ribosomal protein S1; Provisional |
630-710 | 6.36e-04 | |||||||||||
bifunctional cytidylate kinase/ribosomal protein S1; Provisional Pssm-ID: 105491 [Multi-domain] Cd Length: 863 Bit Score: 43.55 E-value: 6.36e-04
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| PRK08059 | PRK08059 | general stress protein 13; Validated |
630-729 | 1.01e-03 | |||||||||||
general stress protein 13; Validated Pssm-ID: 181215 [Multi-domain] Cd Length: 123 Bit Score: 39.64 E-value: 1.01e-03
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| OB_Dis3 | pfam17849 | Dis3-like cold-shock domain 2 (CSD2); This domain has an OB fold and is found in the Dis3l2 ... |
155-223 | 1.29e-03 | |||||||||||
Dis3-like cold-shock domain 2 (CSD2); This domain has an OB fold and is found in the Dis3l2 protein. This domain along with CSD1 binds to RNA. Pssm-ID: 436091 [Multi-domain] Cd Length: 77 Bit Score: 37.97 E-value: 1.29e-03
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| PRK00087 | PRK00087 | bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1; |
606-700 | 1.59e-03 | |||||||||||
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1; Pssm-ID: 234623 [Multi-domain] Cd Length: 647 Bit Score: 41.86 E-value: 1.59e-03
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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 ... |
629-702 | 1.67e-03 | |||||||||||
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: 37.95 E-value: 1.67e-03
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| S1_Rrp5_repeat_hs12_sc9 | cd05703 | S1_Rrp5_repeat_hs12_sc9: Rrp5 is a trans-acting factor important for biogenesis of both the ... |
631-707 | 2.39e-03 | |||||||||||
S1_Rrp5_repeat_hs12_sc9: 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 12 (hs12) and S. cerevisiae S1 repeat 9 (sc9). Rrp5 is found in eukaryotes but not in prokaryotes or archaea. Pssm-ID: 240208 [Multi-domain] Cd Length: 73 Bit Score: 37.17 E-value: 2.39e-03
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| S1_Rrp5_repeat_hs11_sc8 | cd05702 | S1_Rrp5_repeat_hs11_sc8: Rrp5 is a trans-acting factor important for biogenesis of both the ... |
631-696 | 3.12e-03 | |||||||||||
S1_Rrp5_repeat_hs11_sc8: 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 11 (hs11) and S. cerevisiae S1 repeat 8 (sc8). Rrp5 is found in eukaryotes but not in prokaryotes or archaea. Pssm-ID: 240207 [Multi-domain] Cd Length: 70 Bit Score: 36.80 E-value: 3.12e-03
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| PLN00207 | PLN00207 | polyribonucleotide nucleotidyltransferase; Provisional |
615-745 | 4.30e-03 | |||||||||||
polyribonucleotide nucleotidyltransferase; Provisional Pssm-ID: 215104 [Multi-domain] Cd Length: 891 Bit Score: 40.65 E-value: 4.30e-03
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| S1_pNO40 | cd05686 | S1_pNO40: pNO40 , S1-like RNA-binding domain. pNO40 is a nucleolar protein of unknown function ... |
634-705 | 7.28e-03 | |||||||||||
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: 35.92 E-value: 7.28e-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 ... |
636-706 | 7.39e-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: 35.66 E-value: 7.39e-03
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| S1_RecJ_like | cd04473 | S1_RecJ_like: The S1 domain of the archaea-specific RecJ-like exonuclease. The function of ... |
630-711 | 7.58e-03 | |||||||||||
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: 36.05 E-value: 7.58e-03
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| PRK07252 | PRK07252 | S1 RNA-binding domain-containing protein; |
630-703 | 8.02e-03 | |||||||||||
S1 RNA-binding domain-containing protein; Pssm-ID: 180908 [Multi-domain] Cd Length: 120 Bit Score: 36.99 E-value: 8.02e-03
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