ATP-dependent RNA helicase DHX8 isoform X3 [Macaca mulatta]
Protein Classification
List of domain hits
| Name | Accession | Description | Interval | E-value | |||||||||
| HrpA super family | cl34328 | HrpA-like RNA helicase [Translation, ribosomal structure and biogenesis]; |
558-1144 | 0e+00 | |||||||||
HrpA-like RNA helicase [Translation, ribosomal structure and biogenesis]; The actual alignment was detected with superfamily member COG1643: Pssm-ID: 441249 [Multi-domain] Cd Length: 836 Bit Score: 563.17 E-value: 0e+00
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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 ... |
267-345 | 1.02e-42 | |||||||||
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: 150.08 E-value: 1.02e-42
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| GH2-like_DHX8 | cd21691 | GIPC-homology 2 (GH2)-like domain found in DEAH box protein 8 (DHX8) and similar proteins; ... |
25-92 | 2.74e-40 | |||||||||
GIPC-homology 2 (GH2)-like domain found in DEAH box protein 8 (DHX8) and similar proteins; DHX8 (a human homolog of yeast Prp22), also called RNA helicase HRH1, is an ATP-dependent RNA helicase involved in pre-mRNA splicing as a component of the spliceosome. It facilitates nuclear export of spliced mRNA by releasing the RNA from the spliceosome. This model corresponds to the GH2-like domain that shows high sequence similarity with the GH2 domain found in GIPC (GAIP C-terminus-interacting protein) family of proteins, which mediate endocytosis by tethering cargo proteins to the motor myosin VI. : Pssm-ID: 409668 Cd Length: 68 Bit Score: 142.68 E-value: 2.74e-40
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| Name | Accession | Description | Interval | E-value | |||||||||
| HrpA | COG1643 | HrpA-like RNA helicase [Translation, ribosomal structure and biogenesis]; |
558-1144 | 0e+00 | |||||||||
HrpA-like RNA helicase [Translation, ribosomal structure and biogenesis]; Pssm-ID: 441249 [Multi-domain] Cd Length: 836 Bit Score: 563.17 E-value: 0e+00
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| DEAH_box_HrpA | TIGR01967 | RNA helicase HrpA; This model represents HrpA, one of two related but uncharacterized DEAH-box ... |
565-1151 | 1.78e-146 | |||||||||
RNA helicase HrpA; This model represents HrpA, one of two related but uncharacterized DEAH-box ATP-dependent helicases in many Proteobacteria and a few high-GC Gram-positive bacteria. HrpA is about 1300 amino acids long, while its paralog HrpB, also uncharacterized, is about 800 amino acids long. Related characterized eukarotic proteins are RNA helicases associated with pre-mRNA processing. The HrpA/B homolog from Borrelia is 500 amino acids shorter but appears to be derived from HrpA rather than HrpB. [Unknown function, Enzymes of unknown specificity] Pssm-ID: 273900 [Multi-domain] Cd Length: 1283 Bit Score: 473.49 E-value: 1.78e-146
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| PRK11131 | PRK11131 | ATP-dependent RNA helicase HrpA; Provisional |
565-1148 | 4.08e-139 | |||||||||
ATP-dependent RNA helicase HrpA; Provisional Pssm-ID: 182986 [Multi-domain] Cd Length: 1294 Bit Score: 453.75 E-value: 4.08e-139
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| DEXHc_DHX8 | cd17971 | DEXH-box helicase domain of DEAH-box helicase 8; DEAH-box helicase 8 (DHX8 ,also known as ... |
562-740 | 1.51e-127 | |||||||||
DEXH-box helicase domain of DEAH-box helicase 8; DEAH-box helicase 8 (DHX8 ,also known as pre-mRNA-splicing factor ATP-dependent RNA helicase PRP22) acts late in the splicing of pre-mRNA and mediates the release of the spliced mRNA from spliceosomes. DHX8 belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350729 [Multi-domain] Cd Length: 179 Bit Score: 387.22 E-value: 1.51e-127
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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 ... |
267-345 | 1.02e-42 | |||||||||
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: 150.08 E-value: 1.02e-42
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| GH2-like_DHX8 | cd21691 | GIPC-homology 2 (GH2)-like domain found in DEAH box protein 8 (DHX8) and similar proteins; ... |
25-92 | 2.74e-40 | |||||||||
GIPC-homology 2 (GH2)-like domain found in DEAH box protein 8 (DHX8) and similar proteins; DHX8 (a human homolog of yeast Prp22), also called RNA helicase HRH1, is an ATP-dependent RNA helicase involved in pre-mRNA splicing as a component of the spliceosome. It facilitates nuclear export of spliced mRNA by releasing the RNA from the spliceosome. This model corresponds to the GH2-like domain that shows high sequence similarity with the GH2 domain found in GIPC (GAIP C-terminus-interacting protein) family of proteins, which mediate endocytosis by tethering cargo proteins to the motor myosin VI. Pssm-ID: 409668 Cd Length: 68 Bit Score: 142.68 E-value: 2.74e-40
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| HA2 | smart00847 | Helicase associated domain (HA2) Add an annotation; This presumed domain is about 90 amino ... |
966-1048 | 9.94e-34 | |||||||||
Helicase associated domain (HA2) Add an annotation; This presumed domain is about 90 amino acid residues in length. It is found is a diverse set of RNA helicases. Its function is unknown, however it seems likely to be involved in nucleic acid binding. Pssm-ID: 214852 [Multi-domain] Cd Length: 82 Bit Score: 124.30 E-value: 9.94e-34
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| HA2 | pfam04408 | Helicase associated domain (HA2); This presumed domain is about 90 amino acid residues in ... |
959-1047 | 1.36e-31 | |||||||||
Helicase associated domain (HA2); This presumed domain is about 90 amino acid residues in length. It is found is a diverse set of RNA helicases. Its function is unknown, however it seems likely to be involved in nucleic acid binding. Pssm-ID: 461295 [Multi-domain] Cd Length: 104 Bit Score: 119.26 E-value: 1.36e-31
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| PRK11824 | PRK11824 | polynucleotide phosphorylase/polyadenylase; Provisional |
263-341 | 2.49e-21 | |||||||||
polynucleotide phosphorylase/polyadenylase; Provisional Pssm-ID: 236995 [Multi-domain] Cd Length: 693 Bit Score: 100.12 E-value: 2.49e-21
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| YabR | COG1098 | Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function ... |
262-355 | 2.92e-20 | |||||||||
Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function prediction only]; Pssm-ID: 440715 [Multi-domain] Cd Length: 130 Bit Score: 87.93 E-value: 2.92e-20
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| S1_dom_CvfD | NF040579 | CvfD/Ygs/GSP13 family RNA-binding post-transcriptional regulator; CvfD, Ygs, and GSP13 form a ... |
266-354 | 4.52e-19 | |||||||||
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: 83.63 E-value: 4.52e-19
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| S1 | smart00316 | Ribosomal protein S1-like RNA-binding domain; |
266-338 | 3.92e-14 | |||||||||
Ribosomal protein S1-like RNA-binding domain; Pssm-ID: 197648 [Multi-domain] Cd Length: 72 Bit Score: 68.40 E-value: 3.92e-14
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| S1 | pfam00575 | S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ... |
264-326 | 1.46e-10 | |||||||||
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: 58.07 E-value: 1.46e-10
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| rpsA | TIGR00717 | ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ... |
262-338 | 6.35e-09 | |||||||||
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: 59.75 E-value: 6.35e-09
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| Name | Accession | Description | Interval | E-value | |||||||||
| HrpA | COG1643 | HrpA-like RNA helicase [Translation, ribosomal structure and biogenesis]; |
558-1144 | 0e+00 | |||||||||
HrpA-like RNA helicase [Translation, ribosomal structure and biogenesis]; Pssm-ID: 441249 [Multi-domain] Cd Length: 836 Bit Score: 563.17 E-value: 0e+00
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| DEAH_box_HrpA | TIGR01967 | RNA helicase HrpA; This model represents HrpA, one of two related but uncharacterized DEAH-box ... |
565-1151 | 1.78e-146 | |||||||||
RNA helicase HrpA; This model represents HrpA, one of two related but uncharacterized DEAH-box ATP-dependent helicases in many Proteobacteria and a few high-GC Gram-positive bacteria. HrpA is about 1300 amino acids long, while its paralog HrpB, also uncharacterized, is about 800 amino acids long. Related characterized eukarotic proteins are RNA helicases associated with pre-mRNA processing. The HrpA/B homolog from Borrelia is 500 amino acids shorter but appears to be derived from HrpA rather than HrpB. [Unknown function, Enzymes of unknown specificity] Pssm-ID: 273900 [Multi-domain] Cd Length: 1283 Bit Score: 473.49 E-value: 1.78e-146
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| PRK11131 | PRK11131 | ATP-dependent RNA helicase HrpA; Provisional |
565-1148 | 4.08e-139 | |||||||||
ATP-dependent RNA helicase HrpA; Provisional Pssm-ID: 182986 [Multi-domain] Cd Length: 1294 Bit Score: 453.75 E-value: 4.08e-139
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| DEXHc_DHX8 | cd17971 | DEXH-box helicase domain of DEAH-box helicase 8; DEAH-box helicase 8 (DHX8 ,also known as ... |
562-740 | 1.51e-127 | |||||||||
DEXH-box helicase domain of DEAH-box helicase 8; DEAH-box helicase 8 (DHX8 ,also known as pre-mRNA-splicing factor ATP-dependent RNA helicase PRP22) acts late in the splicing of pre-mRNA and mediates the release of the spliced mRNA from spliceosomes. DHX8 belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350729 [Multi-domain] Cd Length: 179 Bit Score: 387.22 E-value: 1.51e-127
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| DEAH_box_HrpB | TIGR01970 | ATP-dependent helicase HrpB; This model represents HrpB, one of two related but ... |
567-1014 | 1.21e-104 | |||||||||
ATP-dependent helicase HrpB; This model represents HrpB, one of two related but uncharacterized DEAH-box ATP-dependent helicases in many Proteobacteria, but also in a few species of other lineages. The member from Rhizobium meliloti has been designated HelO. HrpB is typically about 800 residues in length, while its paralog HrpA (TIGR01967), also uncharacterized, is about 1300 amino acids long. Related characterized eukarotic proteins are RNA helicases associated with pre-mRNA processing. [Unknown function, Enzymes of unknown specificity] Pssm-ID: 273901 [Multi-domain] Cd Length: 819 Bit Score: 348.68 E-value: 1.21e-104
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| PRK11664 | PRK11664 | ATP-dependent RNA helicase HrpB; Provisional |
566-996 | 5.08e-95 | |||||||||
ATP-dependent RNA helicase HrpB; Provisional Pssm-ID: 236950 [Multi-domain] Cd Length: 812 Bit Score: 322.26 E-value: 5.08e-95
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| DEXHc_DHX38 | cd17983 | DEXH-box helicase domain of DEAH-box helicase 38; DEAH-box helicase 38 (DHX38, also known as ... |
567-739 | 1.81e-94 | |||||||||
DEXH-box helicase domain of DEAH-box helicase 38; DEAH-box helicase 38 (DHX38, also known as PRP16) is involved in pre-mRNA splicing. DHX38 belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350741 [Multi-domain] Cd Length: 173 Bit Score: 298.61 E-value: 1.81e-94
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| DEXHc_DHX16 | cd17974 | DEXH-box helicase domain of DEAH-box helicase 16; DEAH-box helicase 16 (DHX16) is probably ... |
567-739 | 2.11e-89 | |||||||||
DEXH-box helicase domain of DEAH-box helicase 16; DEAH-box helicase 16 (DHX16) is probably involved in pre-mRNA splicing. DHX16 belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350732 [Multi-domain] Cd Length: 174 Bit Score: 285.17 E-value: 2.11e-89
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| DEXHc_RHA-like | cd17917 | DEXH-box helicase domain of DEAD-like helicase RHA family proteins; The RNA helicase A (RHA) ... |
583-739 | 9.59e-88 | |||||||||
DEXH-box helicase domain of DEAD-like helicase RHA family proteins; The RNA helicase A (RHA) family includes RHA, also called DEAH-box helicase 9 (DHX9), DHX8, DHX15-16, DHX32-38, and many others. The RHA family belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 438707 [Multi-domain] Cd Length: 159 Bit Score: 279.73 E-value: 9.59e-88
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| SF2_C_RHA | cd18791 | C-terminal helicase domain of the RNA helicase A (RHA) family helicases; The RNA helicase A ... |
744-905 | 1.27e-86 | |||||||||
C-terminal helicase domain of the RNA helicase A (RHA) family helicases; The RNA helicase A (RHA) family includes RHA, also called DEAH-box helicase 9 (DHX9), DHX8, DHX15-16, DHX32-38, and many others. The RHA family members are DEAD-like helicases belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC. Pssm-ID: 350178 [Multi-domain] Cd Length: 171 Bit Score: 277.49 E-value: 1.27e-86
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| DEXHc_DHX33 | cd17978 | DEXH-box helicase domain of DEAH-box helicase 33; DEAH-box helicase 33 (DHX33) stimulates RNA ... |
567-739 | 3.05e-86 | |||||||||
DEXH-box helicase domain of DEAH-box helicase 33; DEAH-box helicase 33 (DHX33) stimulates RNA polymerase I transcription of the 47S precursor rRNA. DHX33 belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 438710 [Multi-domain] Cd Length: 178 Bit Score: 276.54 E-value: 3.05e-86
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| DEXHc_DHX15 | cd17973 | DEXH-box helicase domain of DEAH-box helicase 15; DEAH-box helicase 15 (DHX15) is a pre-mRNA ... |
560-739 | 1.74e-83 | |||||||||
DEXH-box helicase domain of DEAH-box helicase 15; DEAH-box helicase 15 (DHX15) is a pre-mRNA processing factor involved in disassembly of spliceosomes after the release of mature mRNA. DHX15 belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 438709 [Multi-domain] Cd Length: 187 Bit Score: 269.29 E-value: 1.74e-83
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| DEXHc_DHX35 | cd17980 | DEXH-box helicase domain of DEAH-box helicase 35; DHX35 plays a role in colorectal cancers and ... |
567-731 | 6.55e-76 | |||||||||
DEXH-box helicase domain of DEAH-box helicase 35; DHX35 plays a role in colorectal cancers and seems to be associated with risk to thyroid cancers. It also has been shown to positively regulate poxviruses, such as Myxoma virus. DEAH-box helicase 35 (DHX35) belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350738 [Multi-domain] Cd Length: 185 Bit Score: 248.54 E-value: 6.55e-76
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| DEXHc_DHX40 | cd17984 | DEXH-box helicase domain of DEAH-box helicase 40; DEAH-box helicase 40 (DHX40) belongs to the ... |
567-739 | 2.14e-75 | |||||||||
DEXH-box helicase domain of DEAH-box helicase 40; DEAH-box helicase 40 (DHX40) belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350742 [Multi-domain] Cd Length: 178 Bit Score: 246.69 E-value: 2.14e-75
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| DEXHc_HrpA | cd17989 | DEXH-box helicase domain of ATP-dependent RNA helicase HrpA; HrpA is part of the HrpB-HrpA ... |
567-736 | 3.83e-60 | |||||||||
DEXH-box helicase domain of ATP-dependent RNA helicase HrpA; HrpA is part of the HrpB-HrpA two-partner secretion (TPS) system, a secretion pathway important to the secretion of large virulence-associated proteins. HrpA belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350747 [Multi-domain] Cd Length: 173 Bit Score: 203.46 E-value: 3.83e-60
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| DEXHc_DHX37 | cd17982 | DEXH-box helicase domain of DEAH-box helicase 37; DHX37 plays a role in the development of the ... |
567-729 | 8.50e-58 | |||||||||
DEXH-box helicase domain of DEAH-box helicase 37; DHX37 plays a role in the development of the human nervous system and has been linked to schizophrenia. It also negatively regulates poxviruses such as Myxoma virus. DEAH-box helicase 37 (DHX37) belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350740 [Multi-domain] Cd Length: 191 Bit Score: 197.58 E-value: 8.50e-58
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| DEXHc_DHX34 | cd17979 | DEXH-box helicase domain of DEAH-box helicase 34; DEAH-box helicase 34 (DHX34) plays a role in ... |
567-736 | 1.82e-54 | |||||||||
DEXH-box helicase domain of DEAH-box helicase 34; DEAH-box helicase 34 (DHX34) plays a role in the nonsense-mediated decay (NMD), a surveillance mechanism that degrades aberrant mRNAs. DHX34 belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350737 [Multi-domain] Cd Length: 170 Bit Score: 187.26 E-value: 1.82e-54
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| DEXHc_DHX36 | cd17981 | DEXH-box helicase domain of DEAH-box helicase 36; DEAH-box helicase 36 (DHX36, also known as ... |
567-739 | 1.40e-47 | |||||||||
DEXH-box helicase domain of DEAH-box helicase 36; DEAH-box helicase 36 (DHX36, also known as G4-resolvase 1 or G4R1, MLE-like protein 1 and RNA helicase associated with AU-rich element or RHAU) unwinds a G4-quadruplex in human telomerase RNA. DHX36 belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350739 [Multi-domain] Cd Length: 180 Bit Score: 167.71 E-value: 1.40e-47
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| DEXHc_DHX29 | cd17975 | DEXH-box helicase domain of DEAH-box helicase 29; DEAH-box helicase 29 (DHX29) is a part of ... |
567-739 | 6.62e-47 | |||||||||
DEXH-box helicase domain of DEAH-box helicase 29; DEAH-box helicase 29 (DHX29) is a part of the 43S pre-initiation complex involved in translation initiation of mRNAs with structured 5'-UTRs. DHX29 is part of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350733 [Multi-domain] Cd Length: 183 Bit Score: 166.24 E-value: 6.62e-47
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| DEXHc_YTHDC2 | cd17987 | DEXH-box helicase domain of YTH domain containing 2; YTH domain containing 2 (YTHDC2) ... |
567-739 | 4.18e-46 | |||||||||
DEXH-box helicase domain of YTH domain containing 2; YTH domain containing 2 (YTHDC2) regulates mRNA translation and stability via binding to N6-methyladenosine, a modified RNA nucleotide enriched in the stop codons and 3' UTRs of eukaryotic messenger RNAs. YTHDC2 belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350745 [Multi-domain] Cd Length: 176 Bit Score: 163.46 E-value: 4.18e-46
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| DEXHc_DHX9 | cd17972 | DEXH-box helicase domain of DEAH-box helicase 9; DEAH-box helicase 9 (DHX9, also known as ... |
560-739 | 7.63e-43 | |||||||||
DEXH-box helicase domain of DEAH-box helicase 9; DEAH-box helicase 9 (DHX9, also known as ATP-dependent RNA helicase A or RHA and leukophysin or LKP) plays an important role in many cellular processes, including regulation of DNA replication, transcription, translation, microRNA biogenesis, RNA processing and transport, and maintenance of genomic stability. DHX9 belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350730 [Multi-domain] Cd Length: 234 Bit Score: 156.53 E-value: 7.63e-43
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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 ... |
267-345 | 1.02e-42 | |||||||||
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: 150.08 E-value: 1.02e-42
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| DEXHc_DHX32 | cd17977 | DEXH-box helicase domain of DEAH-box helicase 32; DEAH-box helicase 32 (DHX32) belongs to the ... |
567-736 | 2.74e-42 | |||||||||
DEXH-box helicase domain of DEAH-box helicase 32; DEAH-box helicase 32 (DHX32) belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350735 [Multi-domain] Cd Length: 176 Bit Score: 152.67 E-value: 2.74e-42
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| DEXHc_HrpB | cd17990 | DEXH-box helicase domain of ATP-dependent helicase HrpB; HrpB is part of the HrpB-HrpA ... |
567-737 | 9.34e-42 | |||||||||
DEXH-box helicase domain of ATP-dependent helicase HrpB; HrpB is part of the HrpB-HrpA two-partner secretion (TPS) system, a secretion pathway important to the secretion of large virulence-associated proteins. HrpB belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 438711 [Multi-domain] Cd Length: 174 Bit Score: 150.95 E-value: 9.34e-42
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| DEXHc_DHX57 | cd17985 | DEXH-box helicase domain of DEAH-box helicase 57; DEAH-box helicase 57 (DHX57) belongs to the ... |
567-739 | 6.11e-41 | |||||||||
DEXH-box helicase domain of DEAH-box helicase 57; DEAH-box helicase 57 (DHX57) belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350743 [Multi-domain] Cd Length: 177 Bit Score: 148.84 E-value: 6.11e-41
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| GH2-like_DHX8 | cd21691 | GIPC-homology 2 (GH2)-like domain found in DEAH box protein 8 (DHX8) and similar proteins; ... |
25-92 | 2.74e-40 | |||||||||
GIPC-homology 2 (GH2)-like domain found in DEAH box protein 8 (DHX8) and similar proteins; DHX8 (a human homolog of yeast Prp22), also called RNA helicase HRH1, is an ATP-dependent RNA helicase involved in pre-mRNA splicing as a component of the spliceosome. It facilitates nuclear export of spliced mRNA by releasing the RNA from the spliceosome. This model corresponds to the GH2-like domain that shows high sequence similarity with the GH2 domain found in GIPC (GAIP C-terminus-interacting protein) family of proteins, which mediate endocytosis by tethering cargo proteins to the motor myosin VI. Pssm-ID: 409668 Cd Length: 68 Bit Score: 142.68 E-value: 2.74e-40
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| DEXHc_TDRD9 | cd17988 | DEXH-box helicase domain of tudor domain containing 9; Tudor domain containing 9 (TDRD9, also ... |
567-739 | 1.02e-39 | |||||||||
DEXH-box helicase domain of tudor domain containing 9; Tudor domain containing 9 (TDRD9, also known as HIG-1or NET54 or C14orf75) is a part of the nuclear PIWI-interacting RNA (piRNA) pathway essential for transposon silencing and male fertility TDRD9 belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350746 [Multi-domain] Cd Length: 180 Bit Score: 145.34 E-value: 1.02e-39
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| DEXQc_DQX1 | cd17986 | DEXQ-box helicase domain of DEAQ-box RNA dependent ATPase 1; DEAQ-box RNA dependent ATPase 1 ... |
567-739 | 3.38e-39 | |||||||||
DEXQ-box helicase domain of DEAQ-box RNA dependent ATPase 1; DEAQ-box RNA dependent ATPase 1 (DQX1) belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350744 [Multi-domain] Cd Length: 177 Bit Score: 143.88 E-value: 3.38e-39
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| DEXHc_DHX30 | cd17976 | DEXH-box helicase domain of DEAH-box helicase 30; DEAH-box helicase 30 (DHX30) plays an ... |
567-736 | 6.80e-37 | |||||||||
DEXH-box helicase domain of DEAH-box helicase 30; DEAH-box helicase 30 (DHX30) plays an important role in the assembly of the mitochondrial large ribosomal subunit. DHX30 belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350734 [Multi-domain] Cd Length: 178 Bit Score: 137.23 E-value: 6.80e-37
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| HA2 | smart00847 | Helicase associated domain (HA2) Add an annotation; This presumed domain is about 90 amino ... |
966-1048 | 9.94e-34 | |||||||||
Helicase associated domain (HA2) Add an annotation; This presumed domain is about 90 amino acid residues in length. It is found is a diverse set of RNA helicases. Its function is unknown, however it seems likely to be involved in nucleic acid binding. Pssm-ID: 214852 [Multi-domain] Cd Length: 82 Bit Score: 124.30 E-value: 9.94e-34
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| HA2 | pfam04408 | Helicase associated domain (HA2); This presumed domain is about 90 amino acid residues in ... |
959-1047 | 1.36e-31 | |||||||||
Helicase associated domain (HA2); This presumed domain is about 90 amino acid residues in length. It is found is a diverse set of RNA helicases. Its function is unknown, however it seems likely to be involved in nucleic acid binding. Pssm-ID: 461295 [Multi-domain] Cd Length: 104 Bit Score: 119.26 E-value: 1.36e-31
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| DEXDc | smart00487 | DEAD-like helicases superfamily; |
563-748 | 4.37e-27 | |||||||||
DEAD-like helicases superfamily; Pssm-ID: 214692 [Multi-domain] Cd Length: 201 Bit Score: 109.89 E-value: 4.37e-27
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| GH2_like | cd21690 | GIPC homology 2 (GH2) domain-like family; The GIPC (GAIP C-terminus-interacting protein) ... |
28-89 | 1.20e-23 | |||||||||
GIPC homology 2 (GH2) domain-like family; The GIPC (GAIP C-terminus-interacting protein) family of proteins mediate endocytosis by tethering cargo proteins to the motor myosin VI. This model represents the C-terminal GIPC homology 2 or GH2 domain (plus the linker to the PDZ domain located N-terminally of GH2), which mediates the interaction with myosin VI and is involved in homodimerization in the autoinhibited state. The family also includes DEAH box protein 8 (DHX8) and similar proteins. DHX8 (a human homolog of yeast Prp22), also called RNA helicase HRH1, is an ATP-dependent RNA helicase involved in pre-mRNA splicing as a component of the spliceosome. It facilitates nuclear export of spliced mRNA by releasing the RNA from the spliceosome. DHX8 contains a GH2-like domain at the N-terminus, which shows high sequence similarity with the GH2 domain found in GIPC proteins. Pssm-ID: 409667 Cd Length: 62 Bit Score: 95.23 E-value: 1.20e-23
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| PRK11824 | PRK11824 | polynucleotide phosphorylase/polyadenylase; Provisional |
263-341 | 2.49e-21 | |||||||||
polynucleotide phosphorylase/polyadenylase; Provisional Pssm-ID: 236995 [Multi-domain] Cd Length: 693 Bit Score: 100.12 E-value: 2.49e-21
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| S1_PNPase | cd04472 | S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a ... |
267-337 | 1.62e-20 | |||||||||
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: 86.44 E-value: 1.62e-20
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| YabR | COG1098 | Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function ... |
262-355 | 2.92e-20 | |||||||||
Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function prediction only]; Pssm-ID: 440715 [Multi-domain] Cd Length: 130 Bit Score: 87.93 E-value: 2.92e-20
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| S1_dom_CvfD | NF040579 | CvfD/Ygs/GSP13 family RNA-binding post-transcriptional regulator; CvfD, Ygs, and GSP13 form a ... |
266-354 | 4.52e-19 | |||||||||
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: 83.63 E-value: 4.52e-19
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| RpsA | COG0539 | Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ... |
266-340 | 1.50e-18 | |||||||||
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: 88.56 E-value: 1.50e-18
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| RpsA | COG0539 | Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ... |
266-339 | 9.94e-17 | |||||||||
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: 83.17 E-value: 9.94e-17
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| PRK00087 | PRK00087 | bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1; |
261-346 | 2.50e-16 | |||||||||
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1; Pssm-ID: 234623 [Multi-domain] Cd Length: 647 Bit Score: 83.84 E-value: 2.50e-16
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| rpsA | PRK06676 | 30S ribosomal protein S1; Reviewed |
267-366 | 4.26e-15 | |||||||||
30S ribosomal protein S1; Reviewed Pssm-ID: 235851 [Multi-domain] Cd Length: 390 Bit Score: 78.76 E-value: 4.26e-15
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| rpsA | PRK06676 | 30S ribosomal protein S1; Reviewed |
267-340 | 4.79e-15 | |||||||||
30S ribosomal protein S1; Reviewed Pssm-ID: 235851 [Multi-domain] Cd Length: 390 Bit Score: 78.38 E-value: 4.79e-15
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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 ... |
267-338 | 5.61e-15 | |||||||||
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: 70.78 E-value: 5.61e-15
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| HELICc | smart00490 | helicase superfamily c-terminal domain; |
793-897 | 1.01e-14 | |||||||||
helicase superfamily c-terminal domain; Pssm-ID: 197757 [Multi-domain] Cd Length: 82 Bit Score: 70.32 E-value: 1.01e-14
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| S1 | smart00316 | Ribosomal protein S1-like RNA-binding domain; |
266-338 | 3.92e-14 | |||||||||
Ribosomal protein S1-like RNA-binding domain; Pssm-ID: 197648 [Multi-domain] Cd Length: 72 Bit Score: 68.40 E-value: 3.92e-14
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| PRK08059 | PRK08059 | general stress protein 13; Validated |
265-338 | 1.55e-13 | |||||||||
general stress protein 13; Validated Pssm-ID: 181215 [Multi-domain] Cd Length: 123 Bit Score: 68.15 E-value: 1.55e-13
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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 ... |
266-338 | 1.58e-13 | |||||||||
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: 66.50 E-value: 1.58e-13
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| Helicase_C | pfam00271 | Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ... |
763-897 | 1.34e-12 | |||||||||
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, whereas this domain family is found in a wide variety of helicases and helicase related proteins. It may be that this is not an autonomously folding unit, but an integral part of the helicase. Pssm-ID: 459740 [Multi-domain] Cd Length: 109 Bit Score: 65.31 E-value: 1.34e-12
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| PRK08582 | PRK08582 | RNA-binding protein S1; |
272-363 | 3.56e-12 | |||||||||
RNA-binding protein S1; Pssm-ID: 236305 [Multi-domain] Cd Length: 139 Bit Score: 65.05 E-value: 3.56e-12
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| rpsA | PRK06299 | 30S ribosomal protein S1; Reviewed |
266-338 | 6.29e-12 | |||||||||
30S ribosomal protein S1; Reviewed Pssm-ID: 235775 [Multi-domain] Cd Length: 565 Bit Score: 69.81 E-value: 6.29e-12
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| PRK00087 | PRK00087 | bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1; |
267-340 | 2.18e-11 | |||||||||
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1; Pssm-ID: 234623 [Multi-domain] Cd Length: 647 Bit Score: 68.05 E-value: 2.18e-11
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| S1_like | cd00164 | S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ... |
270-337 | 2.37e-11 | |||||||||
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: 60.09 E-value: 2.37e-11
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| rpsA | PRK13806 | 30S ribosomal protein S1; Provisional |
267-340 | 2.72e-11 | |||||||||
30S ribosomal protein S1; Provisional Pssm-ID: 237516 [Multi-domain] Cd Length: 491 Bit Score: 67.44 E-value: 2.72e-11
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| OB_NTP_bind | pfam07717 | Oligonucleotide/oligosaccharide-binding (OB)-fold; This family is found towards the C-terminus ... |
1105-1151 | 1.37e-10 | |||||||||
Oligonucleotide/oligosaccharide-binding (OB)-fold; This family is found towards the C-terminus of the DEAD-box helicases (pfam00270). In these helicases it is apparently always found in association with pfam04408. There do seem to be a couple of instances where it occurs by itself -. The structure PDB:3i4u adopts an OB-fold. helicases (pfam00270). In these helicases it is apparently always found in association with pfam04408. This C-terminal domain of the yeast helicase contains an oligonucleotide/oligosaccharide-binding (OB)-fold which seems to be placed at the entrance of the putative nucleic acid cavity. It also constitutes the binding site for the G-patch-containing domain of Pfa1p. When found on DEAH/RHA helicases, this domain is central to the regulation of the helicase activity through its binding of both RNA and G-patch domain proteins. Pssm-ID: 400182 [Multi-domain] Cd Length: 82 Bit Score: 58.42 E-value: 1.37e-10
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| S1 | pfam00575 | S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ... |
264-326 | 1.46e-10 | |||||||||
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: 58.07 E-value: 1.46e-10
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| PRK07252 | PRK07252 | S1 RNA-binding domain-containing protein; |
266-354 | 4.35e-10 | |||||||||
S1 RNA-binding domain-containing protein; Pssm-ID: 180908 [Multi-domain] Cd Length: 120 Bit Score: 58.56 E-value: 4.35e-10
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| PRK05807 | PRK05807 | RNA-binding protein S1; |
267-351 | 4.84e-10 | |||||||||
RNA-binding protein S1; Pssm-ID: 235614 [Multi-domain] Cd Length: 136 Bit Score: 58.60 E-value: 4.84e-10
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| PRK03987 | PRK03987 | translation initiation factor IF-2 subunit alpha; Validated |
264-343 | 1.40e-09 | |||||||||
translation initiation factor IF-2 subunit alpha; Validated Pssm-ID: 235188 [Multi-domain] Cd Length: 262 Bit Score: 60.22 E-value: 1.40e-09
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| rpsA | PRK06299 | 30S ribosomal protein S1; Reviewed |
267-338 | 1.68e-09 | |||||||||
30S ribosomal protein S1; Reviewed Pssm-ID: 235775 [Multi-domain] Cd Length: 565 Bit Score: 61.72 E-value: 1.68e-09
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| rpsA | PRK13806 | 30S ribosomal protein S1; Provisional |
267-339 | 2.12e-09 | |||||||||
30S ribosomal protein S1; Provisional Pssm-ID: 237516 [Multi-domain] Cd Length: 491 Bit Score: 61.28 E-value: 2.12e-09
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| rpsA | PRK07899 | 30S ribosomal protein S1; Reviewed |
266-350 | 2.64e-09 | |||||||||
30S ribosomal protein S1; Reviewed Pssm-ID: 236126 [Multi-domain] Cd Length: 486 Bit Score: 61.21 E-value: 2.64e-09
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| S1_Tex | cd05685 | S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has ... |
267-327 | 3.63e-09 | |||||||||
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: 54.16 E-value: 3.63e-09
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| Tex | COG2183 | Transcriptional accessory protein Tex/SPT6 [Transcription]; |
266-346 | 5.60e-09 | |||||||||
Transcriptional accessory protein Tex/SPT6 [Transcription]; Pssm-ID: 441786 [Multi-domain] Cd Length: 719 Bit Score: 60.42 E-value: 5.60e-09
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| rpsA | TIGR00717 | ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ... |
262-338 | 6.35e-09 | |||||||||
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: 59.75 E-value: 6.35e-09
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| S1_IF2_alpha | cd04452 | S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain. ... |
264-326 | 8.36e-09 | |||||||||
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: 53.36 E-value: 8.36e-09
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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, ... |
266-327 | 1.02e-08 | |||||||||
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: 53.17 E-value: 1.02e-08
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| PLN00207 | PLN00207 | polyribonucleotide nucleotidyltransferase; Provisional |
264-395 | 1.83e-08 | |||||||||
polyribonucleotide nucleotidyltransferase; Provisional Pssm-ID: 215104 [Multi-domain] Cd Length: 891 Bit Score: 58.75 E-value: 1.83e-08
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| rpsA | TIGR00717 | ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ... |
265-348 | 2.16e-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: 58.21 E-value: 2.16e-08
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| rpsA | PRK06299 | 30S ribosomal protein S1; Reviewed |
266-338 | 2.41e-08 | |||||||||
30S ribosomal protein S1; Reviewed Pssm-ID: 235775 [Multi-domain] Cd Length: 565 Bit Score: 58.25 E-value: 2.41e-08
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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 ... |
265-338 | 3.03e-08 | |||||||||
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: 51.95 E-value: 3.03e-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 ... |
267-337 | 5.01e-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: 50.96 E-value: 5.01e-08
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| rpsA | PRK06299 | 30S ribosomal protein S1; Reviewed |
267-343 | 3.53e-07 | |||||||||
30S ribosomal protein S1; Reviewed Pssm-ID: 235775 [Multi-domain] Cd Length: 565 Bit Score: 54.40 E-value: 3.53e-07
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| PHA02653 | PHA02653 | RNA helicase NPH-II; Provisional |
678-906 | 3.57e-07 | |||||||||
RNA helicase NPH-II; Provisional Pssm-ID: 177443 [Multi-domain] Cd Length: 675 Bit Score: 54.60 E-value: 3.57e-07
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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 ... |
272-337 | 1.06e-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: 47.19 E-value: 1.06e-06
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| VacB | COG0557 | Exoribonuclease R [Transcription]; |
266-327 | 2.42e-06 | |||||||||
Exoribonuclease R [Transcription]; Pssm-ID: 440323 [Multi-domain] Cd Length: 711 Bit Score: 51.65 E-value: 2.42e-06
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| rpsA | PRK07899 | 30S ribosomal protein S1; Reviewed |
267-338 | 4.37e-06 | |||||||||
30S ribosomal protein S1; Reviewed Pssm-ID: 236126 [Multi-domain] Cd Length: 486 Bit Score: 50.81 E-value: 4.37e-06
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| SF2-N | cd00046 | N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ... |
586-721 | 9.28e-06 | |||||||||
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily 2 helicases comprise a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This N-terminal domain contains the ATP-binding region. Pssm-ID: 350668 [Multi-domain] Cd Length: 146 Bit Score: 46.63 E-value: 9.28e-06
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| DEXHc_viral_Ns3 | cd17931 | DEXH-box helicase domain of NS3 protease-helicase; NS3 is a nonstructural multifunctional ... |
592-690 | 1.78e-05 | |||||||||
DEXH-box helicase domain of NS3 protease-helicase; NS3 is a nonstructural multifunctional protein found in pestiviruses that contains an N-terminal protease and a C-terminal helicase. The N-terminal domain is a chymotrypsin-like serine protease, which is responsible for most of the maturation cleavages of the polyprotein precursor in the cytosolic side of the endoplasmic reticulum membrane. The C-terminal domain, about two-thirds of NS3, is a helicase belonging to superfamily 2 (SF2) thought to be important for unwinding highly structured regions of the RNA genome during replication. NS3 plays an essential role in viral polyprotein processing and genome replication. NS3 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350689 [Multi-domain] Cd Length: 151 Bit Score: 46.00 E-value: 1.78e-05
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| rpsA | TIGR00717 | ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ... |
267-338 | 3.50e-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: 47.81 E-value: 3.50e-05
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| PRK12269 | PRK12269 | bifunctional cytidylate kinase/ribosomal protein S1; Provisional |
266-348 | 1.07e-04 | |||||||||
bifunctional cytidylate kinase/ribosomal protein S1; Provisional Pssm-ID: 105491 [Multi-domain] Cd Length: 863 Bit Score: 46.63 E-value: 1.07e-04
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| S1_RNase_E | cd04453 | S1_RNase_E: RNase E and RNase G, S1-like RNA-binding domain. RNase E is an essential ... |
262-332 | 1.85e-04 | |||||||||
S1_RNase_E: RNase E and RNase G, S1-like RNA-binding domain. RNase E is an essential endoribonuclease in the processing and degradation of RNA. In addition to its role in mRNA degradation, RNase E has also been implicated in the processing of rRNA, and the maturation of tRNA, 10Sa RNA and the M1 precursor of RNase P. RNase E associates with PNPase (3' to 5' exonuclease), Rhl B (DEAD-box RNA helicase) and enolase (glycolytic enzyme) to form the RNA degradosome. RNase E tends to cut mRNA within single-stranded regions that are rich in A/U nucleotides. The N-terminal region of RNase E contains the catalytic site. Within the conserved N-terminal domain of RNAse E and RNase G, there is an S1-like subdomain, which is an ancient single-stranded RNA-binding domain. S1 domain is an RNA-binding module originally identified in the ribosomal protein S1. The S1 domain is required for RNA cleavage by RNase E. RNase G is paralogous to RNase E with an N-terminal catalytic domain that is highly homologous to that of RNase E. RNase G not only shares sequence similarity with RNase E, but also functionally overlaps with RNase E. In Escherichia coli, RNase G is involved in the maturation of the 5' end of the 16S rRNA. RNase G plays a secondary role in mRNA decay. Pssm-ID: 239900 [Multi-domain] Cd Length: 88 Bit Score: 41.43 E-value: 1.85e-04
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| SF2_C | cd18785 | C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases ... |
836-905 | 2.09e-04 | |||||||||
C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases include DEAD-box helicases, UvrB, RecG, Ski2, Sucrose Non-Fermenting (SNF) family helicases, and dicer proteins, among others. Similar to SF1 helicases, they do not form toroidal structures like SF3-6 helicases. SF2 helicases are a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Their helicase core is surrounded by C- and N-terminal domains with specific functions such as nucleases, RNA or DNA binding domains, or domains engaged in protein-protein interactions. The core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC. Pssm-ID: 350172 [Multi-domain] Cd Length: 77 Bit Score: 40.77 E-value: 2.09e-04
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| rpsA | PRK06676 | 30S ribosomal protein S1; Reviewed |
262-347 | 1.37e-03 | |||||||||
30S ribosomal protein S1; Reviewed Pssm-ID: 235851 [Multi-domain] Cd Length: 390 Bit Score: 42.55 E-value: 1.37e-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 ... |
262-327 | 1.40e-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: 38.72 E-value: 1.40e-03
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| Cas3_I | cd09639 | CRISPR/Cas system-associated protein Cas3; CRISPR (Clustered Regularly Interspaced Short ... |
585-905 | 2.37e-03 | |||||||||
CRISPR/Cas system-associated protein Cas3; CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; DEAD/DEAH box helicase DNA helicase cas3'; Often but not always is fused to HD nuclease domain; signature gene for Type I Pssm-ID: 187770 [Multi-domain] Cd Length: 353 Bit Score: 41.65 E-value: 2.37e-03
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| AAA_22 | pfam13401 | AAA domain; |
584-690 | 2.53e-03 | |||||||||
AAA domain; Pssm-ID: 379165 [Multi-domain] Cd Length: 129 Bit Score: 39.25 E-value: 2.53e-03
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| rpsA | TIGR00717 | ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ... |
266-338 | 2.61e-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: 41.64 E-value: 2.61e-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 ... |
261-327 | 5.58e-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: 36.82 E-value: 5.58e-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 ... |
267-328 | 6.04e-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: 36.43 E-value: 6.04e-03
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| MYSc_Myo18 | cd01386 | class XVIII myosin, motor domain; Many members of this class contain a N-terminal PDZ domain ... |
563-639 | 8.58e-03 | |||||||||
class XVIII myosin, motor domain; Many members of this class contain a N-terminal PDZ domain which is commonly found in proteins establishing molecular complexes. The motor domain itself does not exhibit ATPase activity, suggesting that it functions as an actin tether protein. It also has two IQ domains that probably bind light chains or related calmodulins and a C-terminal tail with two sections of coiled-coil domains, which are thought to mediate homodimerization. The function of these myosins are largely unknown. The catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Myosins are actin-dependent molecular motors that play important roles in muscle contraction, cell motility, and organelle transport. The head domain is a molecular motor, which utilizes ATP hydrolysis to generate directed movement toward the plus end along actin filaments. A cyclical interaction between myosin and actin provides the driving force. Rates of ATP hydrolysis and consequently the speed of movement along actin filaments vary widely, from about 0.04 micrometer per second for myosin I to 4.5 micrometer per second for myosin II in skeletal muscle. Myosin II moves in discrete steps about 5-10 nm long and generates 1-5 piconewtons of force. Upon ATP binding, the myosin head dissociates from an actin filament. ATP hydrolysis causes the head to pivot and associate with a new actin subunit. The release of Pi causes the head to pivot and move the filament (power stroke). Release of ADP completes the cycle. CyMoBase classifications were used to confirm and identify the myosins in this hierarchy. Pssm-ID: 276837 [Multi-domain] Cd Length: 689 Bit Score: 40.37 E-value: 8.58e-03
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| CafA | COG1530 | Ribonuclease G or E [Translation, ribosomal structure and biogenesis]; |
255-325 | 9.87e-03 | |||||||||
Ribonuclease G or E [Translation, ribosomal structure and biogenesis]; Pssm-ID: 441139 [Multi-domain] Cd Length: 490 Bit Score: 39.75 E-value: 9.87e-03
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