hypothetical protein KGM_204020 [Danaus plexippus plexippus]
Protein Classification
List of domain hits
| Name | Accession | Description | Interval | E-value | ||||||||||
| Pnp super family | cl34166 | Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ... |
42-734 | 0e+00 | ||||||||||
Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]; The actual alignment was detected with superfamily member COG1185: Pssm-ID: 440798 [Multi-domain] Cd Length: 686 Bit Score: 634.35 E-value: 0e+00
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| Name | Accession | Description | Interval | E-value | ||||||||||
| Pnp | COG1185 | Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ... |
42-734 | 0e+00 | ||||||||||
Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]; Pssm-ID: 440798 [Multi-domain] Cd Length: 686 Bit Score: 634.35 E-value: 0e+00
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| PRK11824 | PRK11824 | polynucleotide phosphorylase/polyadenylase; Provisional |
42-735 | 0e+00 | ||||||||||
polynucleotide phosphorylase/polyadenylase; Provisional Pssm-ID: 236995 [Multi-domain] Cd Length: 693 Bit Score: 624.00 E-value: 0e+00
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| polynuc_phos | TIGR03591 | polyribonucleotide nucleotidyltransferase; Members of this protein family are ... |
41-735 | 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: 595.64 E-value: 0e+00
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| RNase_PH_PNPase_1 | cd11363 | Polyribonucleotide nucleotidyltransferase, repeat 1; Polyribonucleotide nucleotidyltransferase ... |
42-259 | 3.63e-102 | ||||||||||
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: 313.30 E-value: 3.63e-102
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| RNase_PH | pfam01138 | 3' exoribonuclease family, domain 1; This family includes 3'-5' exoribonucleases. Ribonuclease ... |
350-477 | 1.04e-16 | ||||||||||
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: 76.86 E-value: 1.04e-16
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| KH | smart00322 | K homology RNA-binding domain; |
588-651 | 2.39e-03 | ||||||||||
K homology RNA-binding domain; Pssm-ID: 197652 [Multi-domain] Cd Length: 68 Bit Score: 36.89 E-value: 2.39e-03
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| Name | Accession | Description | Interval | E-value | |||||||||||
| Pnp | COG1185 | Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ... |
42-734 | 0e+00 | |||||||||||
Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]; Pssm-ID: 440798 [Multi-domain] Cd Length: 686 Bit Score: 634.35 E-value: 0e+00
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| PRK11824 | PRK11824 | polynucleotide phosphorylase/polyadenylase; Provisional |
42-735 | 0e+00 | |||||||||||
polynucleotide phosphorylase/polyadenylase; Provisional Pssm-ID: 236995 [Multi-domain] Cd Length: 693 Bit Score: 624.00 E-value: 0e+00
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| polynuc_phos | TIGR03591 | polyribonucleotide nucleotidyltransferase; Members of this protein family are ... |
41-735 | 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: 595.64 E-value: 0e+00
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| PLN00207 | PLN00207 | polyribonucleotide nucleotidyltransferase; Provisional |
32-735 | 4.44e-107 | |||||||||||
polyribonucleotide nucleotidyltransferase; Provisional Pssm-ID: 215104 [Multi-domain] Cd Length: 891 Bit Score: 347.27 E-value: 4.44e-107
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| RNase_PH_PNPase_1 | cd11363 | Polyribonucleotide nucleotidyltransferase, repeat 1; Polyribonucleotide nucleotidyltransferase ... |
42-259 | 3.63e-102 | |||||||||||
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: 313.30 E-value: 3.63e-102
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| RNase_PH_PNPase_2 | cd11364 | Polyribonucleotide nucleotidyltransferase, repeat 2; Polyribonucleotide nucleotidyltransferase ... |
350-579 | 5.97e-99 | |||||||||||
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: 304.47 E-value: 5.97e-99
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| KH-I_PNPT1 | cd09033 | type I K homology (KH) RNA-binding domain found in mitochondrial polyribonucleotide ... |
584-647 | 7.46e-26 | |||||||||||
type I K homology (KH) RNA-binding domain found in mitochondrial polyribonucleotide nucleotidyltransferase 1 (PNPT1) and similar proteins; PNPT1, also called 3'-5' RNA exonuclease OLD35, or PNPase old-35, or polynucleotide phosphorylase 1, or PNPase 1, or polynucleotide phosphorylase-like protein, is an RNA-binding protein implicated in numerous RNA metabolic processes. It catalyzes the phosphorolysis of single-stranded polyribonucleotides processively in the 3'-to-5' direction. It acts as a mitochondrial intermembrane factor with RNA-processing exoribonulease activity. PNPT1 is a component of the mitochondrial degradosome (mtEXO) complex, that degrades 3' overhang double-stranded RNA with a 3'-to-5' directionality in an ATP-dependent manner. It is involved in the degradation of non-coding mitochondrial transcripts (MT-ncRNA) and tRNA-like molecules and required for correct processing and polyadenylation of mitochondrial mRNAs. PNPT1 also plays a role as a cytoplasmic RNA import factor that mediates the translocation of small RNA components, like the 5S RNA, the RNA subunit of ribonuclease P and the mitochondrial RNA-processing (MRP) RNA, into the mitochondrial matrix. Pssm-ID: 411809 [Multi-domain] Cd Length: 67 Bit Score: 100.73 E-value: 7.46e-26
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| RNase_PH | pfam01138 | 3' exoribonuclease family, domain 1; This family includes 3'-5' exoribonucleases. Ribonuclease ... |
350-477 | 1.04e-16 | |||||||||||
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: 76.86 E-value: 1.04e-16
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| RNase_PH | pfam01138 | 3' exoribonuclease family, domain 1; This family includes 3'-5' exoribonucleases. Ribonuclease ... |
41-157 | 2.43e-16 | |||||||||||
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: 76.09 E-value: 2.43e-16
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| RNase_PH | cd11358 | RNase PH-like 3'-5' exoribonucleases; RNase PH-like 3'-5' exoribonucleases are enzymes that ... |
51-241 | 2.55e-12 | |||||||||||
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: 66.97 E-value: 2.55e-12
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| RNase_PH_C | pfam03725 | 3' exoribonuclease family, domain 2; This family includes 3'-5' exoribonucleases. Ribonuclease ... |
172-237 | 1.50e-10 | |||||||||||
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: 57.59 E-value: 1.50e-10
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| RNase_PH | cd11358 | RNase PH-like 3'-5' exoribonucleases; RNase PH-like 3'-5' exoribonucleases are enzymes that ... |
351-568 | 5.04e-10 | |||||||||||
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: 60.03 E-value: 5.04e-10
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| Rrp42 | COG2123 | Exosome complex RNA-binding protein Rrp42, RNase PH superfamily [Intracellular trafficking, ... |
330-381 | 3.11e-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: 52.50 E-value: 3.11e-07
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| PRK04282 | PRK04282 | exosome complex protein Rrp42; |
330-381 | 1.09e-06 | |||||||||||
exosome complex protein Rrp42; Pssm-ID: 235268 [Multi-domain] Cd Length: 271 Bit Score: 50.65 E-value: 1.09e-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 ... |
330-381 | 1.45e-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: 50.29 E-value: 1.45e-06
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| RNase_PH_RRP41 | cd11370 | RRP41 subunit of eukaryotic exosome; The RRP41 subunit of eukaryotic exosome is a member of ... |
342-381 | 4.82e-06 | |||||||||||
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: 48.31 E-value: 4.82e-06
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| PRK00087 | PRK00087 | bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1; |
662-743 | 2.50e-05 | |||||||||||
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1; Pssm-ID: 234623 [Multi-domain] Cd Length: 647 Bit Score: 47.63 E-value: 2.50e-05
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| KH-I_PNPase | cd02393 | type I K homology (KH) RNA-binding domain found in polyribonucleotide nucleotidyltransferase ... |
588-658 | 1.03e-04 | |||||||||||
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: 40.92 E-value: 1.03e-04
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| RNase_PH_RRP42 | cd11367 | RRP42 subunit of eukaryotic exosome; The RRP42 subunit of eukaryotic exosome is a member of ... |
337-381 | 3.98e-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: 3.98e-04
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| PRK03983 | PRK03983 | exosome complex exonuclease Rrp41; Provisional |
336-381 | 5.36e-04 | |||||||||||
exosome complex exonuclease Rrp41; Provisional Pssm-ID: 235187 [Multi-domain] Cd Length: 244 Bit Score: 42.31 E-value: 5.36e-04
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| RNase_PH_RRP43 | cd11369 | RRP43 subunit of eukaryotic exosome; The RRP43 subunit of eukaryotic exosome is a member of ... |
327-381 | 5.72e-04 | |||||||||||
RRP43 subunit of eukaryotic exosome; The RRP43 subunit of eukaryotic exosome is a member of the RNase_PH family, named after the bacterial Ribonuclease PH, a 3'-5' exoribonuclease. Structurally all members of this family form hexameric rings (trimers of Rrp41-Rrp45, Rrp46-Rrp43, and Mtr3-Rrp42 dimers). The eukaryotic exosome core is composed of six individually encoded RNase PH-like subunits and three additional proteins (Rrp4, Csl4 and Rrp40) that form a stable cap and contain RNA-binding domains. The RNase PH-like subunits are no longer phosphorolytic enzymes, the exosome directly associates with Rrp44 and Rrp6, hydrolytic exoribonucleases related to bacterial RNase II/R and RNase D. The exosome plays an important role in RNA turnover. It plays a crucial role in the maturation of stable RNA species such as rRNA, snRNA and snoRNA, quality control of mRNA, and the degradation of RNA processing by-products and non-coding transcripts. Pssm-ID: 206774 [Multi-domain] Cd Length: 261 Bit Score: 42.54 E-value: 5.72e-04
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| rpsA | PRK06676 | 30S ribosomal protein S1; Reviewed |
662-733 | 6.01e-04 | |||||||||||
30S ribosomal protein S1; Reviewed Pssm-ID: 235851 [Multi-domain] Cd Length: 390 Bit Score: 42.94 E-value: 6.01e-04
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| RpsA | COG0539 | Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ... |
638-739 | 1.07e-03 | |||||||||||
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: 41.95 E-value: 1.07e-03
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| Rph | COG0689 | Ribonuclease PH [Translation, ribosomal structure and biogenesis]; |
342-384 | 1.16e-03 | |||||||||||
Ribonuclease PH [Translation, ribosomal structure and biogenesis]; Pssm-ID: 440453 [Multi-domain] Cd Length: 238 Bit Score: 41.17 E-value: 1.16e-03
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| KH | smart00322 | K homology RNA-binding domain; |
588-651 | 2.39e-03 | |||||||||||
K homology RNA-binding domain; Pssm-ID: 197652 [Multi-domain] Cd Length: 68 Bit Score: 36.89 E-value: 2.39e-03
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| rph | PRK00173 | ribonuclease PH; Reviewed |
342-384 | 2.71e-03 | |||||||||||
ribonuclease PH; Reviewed Pssm-ID: 178914 Cd Length: 238 Bit Score: 40.09 E-value: 2.71e-03
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| RNase_PH_RRP45 | cd11368 | RRP45 subunit of eukaryotic exosome; The RRP45 subunit of eukaryotic exosome is a member of ... |
329-381 | 4.52e-03 | |||||||||||
RRP45 subunit of eukaryotic exosome; The RRP45 subunit of eukaryotic exosome is a member of the RNase_PH family, named after the bacterial Ribonuclease PH, a 3'-5' exoribonuclease. Structurally all members of this family form hexameric rings (trimers of Rrp41-Rrp45, Rrp46-Rrp43, and Mtr3-Rrp42 dimers). The eukaryotic exosome core is composed of six individually encoded RNase PH-like subunits and three additional proteins (Rrp4, Csl4 and Rrp40) that form a stable cap and contain RNA-binding domains. The RNase PH-like subunits are no longer phosphorolytic enzymes, the exosome directly associates with Rrp44 and Rrp6, hydrolytic exoribonucleases related to bacterial RNase II/R and RNase D. The exosome plays an important role in RNA turnover. It plays a crucial role in the maturation of stable RNA species such as rRNA, snRNA and snoRNA, quality control of mRNA, and the degradation of RNA processing by-products and non-coding transcripts. Pssm-ID: 206773 [Multi-domain] Cd Length: 259 Bit Score: 39.43 E-value: 4.52e-03
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| RpsA | COG0539 | Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ... |
662-733 | 4.81e-03 | |||||||||||
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: 40.03 E-value: 4.81e-03
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| rpsA | TIGR00717 | ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ... |
662-739 | 8.05e-03 | |||||||||||
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: 39.33 E-value: 8.05e-03
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| Blast search parameters | ||||
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