Ddx21 protein, partial [Mus musculus]
Protein Classification
DEAD/DEAH box helicase( domain architecture ID 11423699)
DEAD/DEAH box containing ATP-dependent helicase catalyzes the unwinding of DNA or RNA
List of domain hits
| Name | Accession | Description | Interval | E-value | ||||||
| SrmB | COG0513 | Superfamily II DNA and RNA helicase [Replication, recombination and repair]; |
98-484 | 5.55e-146 | ||||||
Superfamily II DNA and RNA helicase [Replication, recombination and repair]; : Pssm-ID: 440279 [Multi-domain] Cd Length: 420 Bit Score: 431.49 E-value: 5.55e-146
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| GUCT_RHII_Gualpha_beta | cd12936 | RNA-binding GUCT domain found in vertebrate RNA helicase II/Gualpha (RH-II/Gualpha), RNA ... |
527-619 | 1.11e-51 | ||||||
RNA-binding GUCT domain found in vertebrate RNA helicase II/Gualpha (RH-II/Gualpha), RNA helicase II/Gubeta (RH-II/Gubeta) and similar proteins; This subfamily corresponds to the Gu C-terminal (GUCT) domain of RH-II/Gualpha and RH-II/Gubeta, two paralogues found in vertebrates. RH-II/Gualpha, also termed nucleolar RNA helicase 2, or DEAD box protein 21, or nucleolar RNA helicase Gu, is a bifunctional enzyme that displays independent RNA-unwinding and RNA-folding activities. It unwinds double-stranded RNA in the 5' to 3' direction in the presence of Mg2+ through the domains in its N-terminal region. In contrast, it folds single-stranded RNA in an ATP-dependent manner and its C-terminal region is responsible for the Mg2+ independent RNA-foldase activity. RH-II/Gualpha consists of a DEAD box helicase domain (DEAD), a helicase conserved C-terminal domain (helicase_C), and a GUCT followed by three FRGQR repeats and one PRGQR sequence. The DEAD and helicase_C domains may play critical roles in the RNA-helicase activity of RH-II/Gualpha. The function of GUCT domain remains unclear. The C-terminal region responsible for the RNA-foldase activity does not overlap with the GUCT domain. RH-II/Gubeta, also termed ATP-dependent RNA helicase DDX50, or DEAD box protein 50, or nucleolar protein Gu2, shows significant sequence homology with RH-II/Gualpha. It contains a DEAD domain, a helicase_C domain, and a GUCT domain followed by an arginine-serine-rich sequence but not (F/P)RGQR repeats in RH-II/Gualpha. Both RH-II/Gualpha and RH-II/Gubeta localize to nucleoli, suggesting roles in ribosomal RNA production, but RH-II/Gubeta also localizes to nuclear speckles containing the splicing factor SC35, suggesting its possible involvement in pre-mRNA splicing. In contrast to RH-II/Gualpha, RH-II/Gubeta has RNA-unwinding activity, but no RNA-folding activity. : Pssm-ID: 240593 Cd Length: 93 Bit Score: 173.79 E-value: 1.11e-51
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| AdoMet_MTases super family | cl17173 | S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; ... |
632-678 | 4.39e-03 | ||||||
S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.). The actual alignment was detected with superfamily member PTZ00146: Pssm-ID: 473071 Cd Length: 293 Bit Score: 39.72 E-value: 4.39e-03
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| Name | Accession | Description | Interval | E-value | ||||||
| SrmB | COG0513 | Superfamily II DNA and RNA helicase [Replication, recombination and repair]; |
98-484 | 5.55e-146 | ||||||
Superfamily II DNA and RNA helicase [Replication, recombination and repair]; Pssm-ID: 440279 [Multi-domain] Cd Length: 420 Bit Score: 431.49 E-value: 5.55e-146
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| DEADc_DDX21_DDX50 | cd17944 | DEAD-box helicase domain of DEAD box proteins 21 and 50; DDX21 (also called Gu-Alpha and ... |
107-308 | 3.28e-144 | ||||||
DEAD-box helicase domain of DEAD box proteins 21 and 50; DDX21 (also called Gu-Alpha and nucleolar RNA helicase 2) is an RNA helicase that acts as a sensor of the transcriptional status of both RNA polymerase (Pol) I and II. It promotes ribosomal RNA (rRNA) processing and transcription from polymerase II (Pol II) and binds various RNAs, such as rRNAs, snoRNAs, 7SK and, at lower extent, mRNAs. DDX50 (also called Gu-Beta, Nucleolar Protein Gu2, and malignant cell derived RNA helicase). DDX21 and DDX50 have similar genomic structures and are in tandem orientation on chromosome 10, suggesting that the two genes arose by gene duplication in evolution. Diseases associated with DDX21 include stomach disease and cerebral creatine deficiency syndrome 3. Diseases associated with DDX50 include rectal disease. Both are members of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. Their name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP- binding region. Pssm-ID: 350702 [Multi-domain] Cd Length: 202 Bit Score: 418.48 E-value: 3.28e-144
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| PRK11776 | PRK11776 | ATP-dependent RNA helicase DbpA; Provisional |
97-479 | 7.15e-96 | ||||||
ATP-dependent RNA helicase DbpA; Provisional Pssm-ID: 236977 [Multi-domain] Cd Length: 460 Bit Score: 303.65 E-value: 7.15e-96
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| DEAD | pfam00270 | DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ... |
121-295 | 2.38e-53 | ||||||
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome biogenesis, nucleocytoplasmic transport, translation, RNA decay and organellar gene expression. Pssm-ID: 425570 [Multi-domain] Cd Length: 165 Bit Score: 180.90 E-value: 2.38e-53
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| GUCT_RHII_Gualpha_beta | cd12936 | RNA-binding GUCT domain found in vertebrate RNA helicase II/Gualpha (RH-II/Gualpha), RNA ... |
527-619 | 1.11e-51 | ||||||
RNA-binding GUCT domain found in vertebrate RNA helicase II/Gualpha (RH-II/Gualpha), RNA helicase II/Gubeta (RH-II/Gubeta) and similar proteins; This subfamily corresponds to the Gu C-terminal (GUCT) domain of RH-II/Gualpha and RH-II/Gubeta, two paralogues found in vertebrates. RH-II/Gualpha, also termed nucleolar RNA helicase 2, or DEAD box protein 21, or nucleolar RNA helicase Gu, is a bifunctional enzyme that displays independent RNA-unwinding and RNA-folding activities. It unwinds double-stranded RNA in the 5' to 3' direction in the presence of Mg2+ through the domains in its N-terminal region. In contrast, it folds single-stranded RNA in an ATP-dependent manner and its C-terminal region is responsible for the Mg2+ independent RNA-foldase activity. RH-II/Gualpha consists of a DEAD box helicase domain (DEAD), a helicase conserved C-terminal domain (helicase_C), and a GUCT followed by three FRGQR repeats and one PRGQR sequence. The DEAD and helicase_C domains may play critical roles in the RNA-helicase activity of RH-II/Gualpha. The function of GUCT domain remains unclear. The C-terminal region responsible for the RNA-foldase activity does not overlap with the GUCT domain. RH-II/Gubeta, also termed ATP-dependent RNA helicase DDX50, or DEAD box protein 50, or nucleolar protein Gu2, shows significant sequence homology with RH-II/Gualpha. It contains a DEAD domain, a helicase_C domain, and a GUCT domain followed by an arginine-serine-rich sequence but not (F/P)RGQR repeats in RH-II/Gualpha. Both RH-II/Gualpha and RH-II/Gubeta localize to nucleoli, suggesting roles in ribosomal RNA production, but RH-II/Gubeta also localizes to nuclear speckles containing the splicing factor SC35, suggesting its possible involvement in pre-mRNA splicing. In contrast to RH-II/Gualpha, RH-II/Gubeta has RNA-unwinding activity, but no RNA-folding activity. Pssm-ID: 240593 Cd Length: 93 Bit Score: 173.79 E-value: 1.11e-51
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| DEXDc | smart00487 | DEAD-like helicases superfamily; |
111-301 | 1.10e-48 | ||||||
DEAD-like helicases superfamily; Pssm-ID: 214692 [Multi-domain] Cd Length: 201 Bit Score: 169.59 E-value: 1.10e-48
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| GUCT | pfam08152 | GUCT (NUC152) domain; This is the C terminal domain found in the RNA helicase II / Gu protein ... |
530-625 | 5.39e-41 | ||||||
GUCT (NUC152) domain; This is the C terminal domain found in the RNA helicase II / Gu protein family. Pssm-ID: 462378 Cd Length: 96 Bit Score: 144.60 E-value: 5.39e-41
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| cas3_core | TIGR01587 | CRISPR-associated helicase Cas3; This model represents the highly conserved core region of an ... |
135-443 | 7.86e-09 | ||||||
CRISPR-associated helicase Cas3; This model represents the highly conserved core region of an alignment of Cas3, a protein found in association with CRISPR repeat elements in a broad range of bacteria and archaea. Cas3 appears to be a helicase, with regions found by pfam00270 (DEAD/DEAH box helicase) and pfam00271 (Helicase conserved C-terminal domain). Some but not all members have an N-terminal HD domain region (pfam01966) that is not included within this model. Pssm-ID: 273707 [Multi-domain] Cd Length: 359 Bit Score: 57.85 E-value: 7.86e-09
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| PTZ00146 | PTZ00146 | fibrillarin; Provisional |
632-678 | 4.39e-03 | ||||||
fibrillarin; Provisional Pssm-ID: 240291 Cd Length: 293 Bit Score: 39.72 E-value: 4.39e-03
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| Name | Accession | Description | Interval | E-value | |||||||
| SrmB | COG0513 | Superfamily II DNA and RNA helicase [Replication, recombination and repair]; |
98-484 | 5.55e-146 | |||||||
Superfamily II DNA and RNA helicase [Replication, recombination and repair]; Pssm-ID: 440279 [Multi-domain] Cd Length: 420 Bit Score: 431.49 E-value: 5.55e-146
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| DEADc_DDX21_DDX50 | cd17944 | DEAD-box helicase domain of DEAD box proteins 21 and 50; DDX21 (also called Gu-Alpha and ... |
107-308 | 3.28e-144 | |||||||
DEAD-box helicase domain of DEAD box proteins 21 and 50; DDX21 (also called Gu-Alpha and nucleolar RNA helicase 2) is an RNA helicase that acts as a sensor of the transcriptional status of both RNA polymerase (Pol) I and II. It promotes ribosomal RNA (rRNA) processing and transcription from polymerase II (Pol II) and binds various RNAs, such as rRNAs, snoRNAs, 7SK and, at lower extent, mRNAs. DDX50 (also called Gu-Beta, Nucleolar Protein Gu2, and malignant cell derived RNA helicase). DDX21 and DDX50 have similar genomic structures and are in tandem orientation on chromosome 10, suggesting that the two genes arose by gene duplication in evolution. Diseases associated with DDX21 include stomach disease and cerebral creatine deficiency syndrome 3. Diseases associated with DDX50 include rectal disease. Both are members of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. Their name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP- binding region. Pssm-ID: 350702 [Multi-domain] Cd Length: 202 Bit Score: 418.48 E-value: 3.28e-144
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| PRK11776 | PRK11776 | ATP-dependent RNA helicase DbpA; Provisional |
97-479 | 7.15e-96 | |||||||
ATP-dependent RNA helicase DbpA; Provisional Pssm-ID: 236977 [Multi-domain] Cd Length: 460 Bit Score: 303.65 E-value: 7.15e-96
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| DEADc | cd00268 | DEAD-box helicase domain of DEAD box helicases; DEAD-box helicases comprise a diverse family ... |
107-301 | 8.17e-87 | |||||||
DEAD-box helicase domain of DEAD box helicases; DEAD-box helicases comprise a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region. Pssm-ID: 350669 [Multi-domain] Cd Length: 196 Bit Score: 270.47 E-value: 8.17e-87
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| PRK11634 | PRK11634 | ATP-dependent RNA helicase DeaD; Provisional |
95-478 | 6.08e-75 | |||||||
ATP-dependent RNA helicase DeaD; Provisional Pssm-ID: 236941 [Multi-domain] Cd Length: 629 Bit Score: 253.23 E-value: 6.08e-75
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| PRK01297 | PRK01297 | ATP-dependent RNA helicase RhlB; Provisional |
29-471 | 1.53e-71 | |||||||
ATP-dependent RNA helicase RhlB; Provisional Pssm-ID: 234938 [Multi-domain] Cd Length: 475 Bit Score: 240.20 E-value: 1.53e-71
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| PTZ00110 | PTZ00110 | helicase; Provisional |
90-461 | 5.78e-64 | |||||||
helicase; Provisional Pssm-ID: 240273 [Multi-domain] Cd Length: 545 Bit Score: 221.57 E-value: 5.78e-64
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| PRK04837 | PRK04837 | ATP-dependent RNA helicase RhlB; Provisional |
92-498 | 3.17e-63 | |||||||
ATP-dependent RNA helicase RhlB; Provisional Pssm-ID: 235314 [Multi-domain] Cd Length: 423 Bit Score: 216.38 E-value: 3.17e-63
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| PRK11192 | PRK11192 | ATP-dependent RNA helicase SrmB; Provisional |
98-448 | 1.12e-62 | |||||||
ATP-dependent RNA helicase SrmB; Provisional Pssm-ID: 236877 [Multi-domain] Cd Length: 434 Bit Score: 215.19 E-value: 1.12e-62
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| DEADc_MSS116 | cd17964 | DEAD-box helicase domain of DEAD-box helicase Mss116; Mss116 is an RNA chaperone important for ... |
103-308 | 2.06e-58 | |||||||
DEAD-box helicase domain of DEAD-box helicase Mss116; Mss116 is an RNA chaperone important for mitochondrial group I and II intron splicing, translational activation, and RNA end processing. Mss116 is a member of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region. Pssm-ID: 350722 [Multi-domain] Cd Length: 211 Bit Score: 196.26 E-value: 2.06e-58
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| PTZ00424 | PTZ00424 | helicase 45; Provisional |
122-464 | 2.43e-56 | |||||||
helicase 45; Provisional Pssm-ID: 185609 [Multi-domain] Cd Length: 401 Bit Score: 196.97 E-value: 2.43e-56
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| PRK04537 | PRK04537 | ATP-dependent RNA helicase RhlB; Provisional |
98-465 | 2.29e-55 | |||||||
ATP-dependent RNA helicase RhlB; Provisional Pssm-ID: 235307 [Multi-domain] Cd Length: 572 Bit Score: 198.64 E-value: 2.29e-55
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| DEAD | pfam00270 | DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ... |
121-295 | 2.38e-53 | |||||||
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome biogenesis, nucleocytoplasmic transport, translation, RNA decay and organellar gene expression. Pssm-ID: 425570 [Multi-domain] Cd Length: 165 Bit Score: 180.90 E-value: 2.38e-53
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| PRK10590 | PRK10590 | ATP-dependent RNA helicase RhlE; Provisional |
97-448 | 3.22e-53 | |||||||
ATP-dependent RNA helicase RhlE; Provisional Pssm-ID: 236722 [Multi-domain] Cd Length: 456 Bit Score: 190.02 E-value: 3.22e-53
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| DEADc_DDX3_DDX4 | cd17967 | DEAD-box helicase domain of ATP-dependent RNA helicases DDX3 and DDX4; This subfamily includes ... |
121-301 | 8.12e-53 | |||||||
DEAD-box helicase domain of ATP-dependent RNA helicases DDX3 and DDX4; This subfamily includes Drosophila melanogaster Vasa, which is essential for development. DEAD box protein 3 (DDX3) has been reported to display a high level of RNA-independent ATPase activity stimulated by both RNA and DNA. DEAD box protein 4 (DDX4, also known as VASA homolog) is an ATP-dependent RNA helicase required during spermatogenesis and is essential for the germline integrity. DDX3 and DDX4 are members of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region. Pssm-ID: 350725 [Multi-domain] Cd Length: 221 Bit Score: 181.53 E-value: 8.12e-53
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| GUCT_RHII_Gualpha_beta | cd12936 | RNA-binding GUCT domain found in vertebrate RNA helicase II/Gualpha (RH-II/Gualpha), RNA ... |
527-619 | 1.11e-51 | |||||||
RNA-binding GUCT domain found in vertebrate RNA helicase II/Gualpha (RH-II/Gualpha), RNA helicase II/Gubeta (RH-II/Gubeta) and similar proteins; This subfamily corresponds to the Gu C-terminal (GUCT) domain of RH-II/Gualpha and RH-II/Gubeta, two paralogues found in vertebrates. RH-II/Gualpha, also termed nucleolar RNA helicase 2, or DEAD box protein 21, or nucleolar RNA helicase Gu, is a bifunctional enzyme that displays independent RNA-unwinding and RNA-folding activities. It unwinds double-stranded RNA in the 5' to 3' direction in the presence of Mg2+ through the domains in its N-terminal region. In contrast, it folds single-stranded RNA in an ATP-dependent manner and its C-terminal region is responsible for the Mg2+ independent RNA-foldase activity. RH-II/Gualpha consists of a DEAD box helicase domain (DEAD), a helicase conserved C-terminal domain (helicase_C), and a GUCT followed by three FRGQR repeats and one PRGQR sequence. The DEAD and helicase_C domains may play critical roles in the RNA-helicase activity of RH-II/Gualpha. The function of GUCT domain remains unclear. The C-terminal region responsible for the RNA-foldase activity does not overlap with the GUCT domain. RH-II/Gubeta, also termed ATP-dependent RNA helicase DDX50, or DEAD box protein 50, or nucleolar protein Gu2, shows significant sequence homology with RH-II/Gualpha. It contains a DEAD domain, a helicase_C domain, and a GUCT domain followed by an arginine-serine-rich sequence but not (F/P)RGQR repeats in RH-II/Gualpha. Both RH-II/Gualpha and RH-II/Gubeta localize to nucleoli, suggesting roles in ribosomal RNA production, but RH-II/Gubeta also localizes to nuclear speckles containing the splicing factor SC35, suggesting its possible involvement in pre-mRNA splicing. In contrast to RH-II/Gualpha, RH-II/Gubeta has RNA-unwinding activity, but no RNA-folding activity. Pssm-ID: 240593 Cd Length: 93 Bit Score: 173.79 E-value: 1.11e-51
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| PLN00206 | PLN00206 | DEAD-box ATP-dependent RNA helicase; Provisional |
98-472 | 5.62e-49 | |||||||
DEAD-box ATP-dependent RNA helicase; Provisional Pssm-ID: 215103 [Multi-domain] Cd Length: 518 Bit Score: 179.60 E-value: 5.62e-49
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| DEXDc | smart00487 | DEAD-like helicases superfamily; |
111-301 | 1.10e-48 | |||||||
DEAD-like helicases superfamily; Pssm-ID: 214692 [Multi-domain] Cd Length: 201 Bit Score: 169.59 E-value: 1.10e-48
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| SF2_C_DEAD | cd18787 | C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse ... |
321-451 | 1.38e-48 | |||||||
C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis, and RNA degradation. They are superfamily (SF)2 helicases that, similar to SF1, 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: 350174 [Multi-domain] Cd Length: 131 Bit Score: 166.53 E-value: 1.38e-48
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| DEADc_DDX54 | cd17959 | DEAD-box helicase domain of DEAD box protein 54; DDX54 interacts in a hormone-dependent manner ... |
96-289 | 7.51e-47 | |||||||
DEAD-box helicase domain of DEAD box protein 54; DDX54 interacts in a hormone-dependent manner with nuclear receptors, and represses their transcriptional activity. DDX54 is a member of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region. Pssm-ID: 350717 [Multi-domain] Cd Length: 205 Bit Score: 164.79 E-value: 7.51e-47
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| DEADc_DDX5_DDX17 | cd17966 | DEAD-box helicase domain of ATP-dependent RNA helicases DDX5 and DDX17; DDX5 and DDX17 are ... |
108-307 | 3.77e-46 | |||||||
DEAD-box helicase domain of ATP-dependent RNA helicases DDX5 and DDX17; DDX5 and DDX17 are members of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region. Pssm-ID: 350724 [Multi-domain] Cd Length: 197 Bit Score: 162.54 E-value: 3.77e-46
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| DEADc_DDX4 | cd18052 | DEAD-box helicase domain of DEAD box protein 4; DEAD box protein 4 (DDX4, also known as VASA ... |
121-304 | 2.70e-45 | |||||||
DEAD-box helicase domain of DEAD box protein 4; DEAD box protein 4 (DDX4, also known as VASA homolog) is an ATP-dependent RNA helicase required during spermatogenesis and is essential for the germline integrity. DEAD-box helicases are a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region. Pssm-ID: 350810 [Multi-domain] Cd Length: 264 Bit Score: 162.44 E-value: 2.70e-45
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| DEADc_DDX6 | cd17940 | DEAD-box helicase domain of DEAD box protein 6; DEAD box protein 6 (DDX6, also known as Rck or ... |
98-305 | 4.00e-45 | |||||||
DEAD-box helicase domain of DEAD box protein 6; DEAD box protein 6 (DDX6, also known as Rck or p54) participates in mRNA regulation mediated by miRNA-mediated silencing. It also plays a role in global and transcript-specific messenger RNA (mRNA) storage, translational repression, and decay. It is a member of the DEAD-box helicase family, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region. Pssm-ID: 350698 [Multi-domain] Cd Length: 201 Bit Score: 159.77 E-value: 4.00e-45
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| DEADc_DDX27 | cd17947 | DEAD-box helicase domain of DEAD box protein 27; DDX27 (also called RHLP, deficiency of ... |
121-287 | 1.46e-43 | |||||||
DEAD-box helicase domain of DEAD box protein 27; DDX27 (also called RHLP, deficiency of ribosomal subunits protein 1 homolog, and probable ATP-dependent RNA helicase DDX27) is involved in the processing of 5.8S and 28S ribosomal RNAs. More specifically, the encoded protein localizes to the nucleolus, where it interacts with the PeBoW complex to ensure proper 3' end formation of 47S rRNA. DDX27 is a member of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region. Pssm-ID: 350705 [Multi-domain] Cd Length: 196 Bit Score: 155.49 E-value: 1.46e-43
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| DEADc_DDX23 | cd17945 | DEAD-box helicase domain of DEAD box protein 23; DDX23 (also called U5 snRNP 100kD protein and ... |
121-302 | 1.54e-43 | |||||||
DEAD-box helicase domain of DEAD box protein 23; DDX23 (also called U5 snRNP 100kD protein and PRP28 homolog) is involved in pre-mRNA splicing and its phosphorylated form (by SRPK2) is required for spliceosomal B complex formation. Diseases associated with DDX23 include distal hereditary motor neuropathy, type II. DDX23 is a member of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region. Pssm-ID: 350703 [Multi-domain] Cd Length: 220 Bit Score: 155.94 E-value: 1.54e-43
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| DEADc_DDX46 | cd17953 | DEAD-box helicase domain of DEAD box protein 46; DDX46 (also called Prp5-like DEAD-box protein) ... |
103-305 | 9.82e-43 | |||||||
DEAD-box helicase domain of DEAD box protein 46; DDX46 (also called Prp5-like DEAD-box protein) is a component of the 17S U2 snRNP complex. It plays an important role in pre-mRNA splicing and has a role in antiviral innate immunity. DDX46 is a member of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region. Pssm-ID: 350711 [Multi-domain] Cd Length: 222 Bit Score: 154.07 E-value: 9.82e-43
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| DEADc_DDX43_DDX53 | cd17958 | DEAD-box helicase domain of DEAD box proteins 43 and 53; DDX43 (also called cancer/testis ... |
121-301 | 3.90e-42 | |||||||
DEAD-box helicase domain of DEAD box proteins 43 and 53; DDX43 (also called cancer/testis antigen 13 or helical antigen) displays tumor-specific expression. Diseases associated with DDX43 include rheumatoid lung disease. DDX53 is also called cancer/testis antigen 26 or DEAD-Box Protein CAGE. Both DDX46 and DDX53 are members of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region. Pssm-ID: 350716 [Multi-domain] Cd Length: 197 Bit Score: 151.46 E-value: 3.90e-42
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| GUCT | pfam08152 | GUCT (NUC152) domain; This is the C terminal domain found in the RNA helicase II / Gu protein ... |
530-625 | 5.39e-41 | |||||||
GUCT (NUC152) domain; This is the C terminal domain found in the RNA helicase II / Gu protein family. Pssm-ID: 462378 Cd Length: 96 Bit Score: 144.60 E-value: 5.39e-41
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| DEADc_EIF4A | cd17939 | DEAD-box helicase domain of eukaryotic initiation factor 4A; The eukaryotic initiation ... |
122-300 | 1.09e-40 | |||||||
DEAD-box helicase domain of eukaryotic initiation factor 4A; The eukaryotic initiation factor-4A (eIF4A) family consists of 3 proteins EIF4A1, EIF4A2, and EIF4A3. These factors are required for the binding of mRNA to 40S ribosomal subunits. In addition these proteins are helicases that function to unwind double-stranded RNA. EIF4A proteins are members of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region. Pssm-ID: 350697 [Multi-domain] Cd Length: 199 Bit Score: 147.47 E-value: 1.09e-40
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| DEADc_DDX5 | cd18049 | DEAD-box helicase domain of DEAD box protein 5; DDX5 (also called RNA helicase P68, HLR1, ... |
121-309 | 9.08e-40 | |||||||
DEAD-box helicase domain of DEAD box protein 5; DDX5 (also called RNA helicase P68, HLR1, G17P1, or HUMP68) is involved in pathways that include the alteration of RNA structures, plays a role as a coregulator of transcription, a regulator of splicing, and in the processing of small noncoding RNAs. It synergizes with DDX17 and SRA1 RNA to activate MYOD1 transcriptional activity and is involved in skeletal muscle differentiation. Dysregulation of this gene may play a role in cancer development. DDX5 is a member of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region. Pssm-ID: 350807 [Multi-domain] Cd Length: 234 Bit Score: 146.31 E-value: 9.08e-40
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| DEADc_DDX10 | cd17941 | DEAD-box helicase domain of DEAD box protein 10; Fusion of the DDX10 gene and the nucleoporin ... |
107-287 | 4.42e-39 | |||||||
DEAD-box helicase domain of DEAD box protein 10; Fusion of the DDX10 gene and the nucleoporin gene, NUP98, by inversion 11 (p15q22) chromosome translocation is found in the patients with de novo or therapy-related myeloid malignancies. Diseases associated with DDX10 (also known as DDX10-NUP98 Fusion Protein Type 2) include myelodysplastic syndrome and leukemia, acute myeloid. DDX10 is a member of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region. Pssm-ID: 350699 [Multi-domain] Cd Length: 198 Bit Score: 142.81 E-value: 4.42e-39
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| DEADc_DDX31 | cd17949 | DEAD-box helicase domain of DEAD box protein 31; DDX31 (also called helicain or G2 helicase) ... |
122-287 | 4.63e-39 | |||||||
DEAD-box helicase domain of DEAD box protein 31; DDX31 (also called helicain or G2 helicase) plays a role in ribosome biogenesis and TP53/p53 regulation through its interaction with NPM1. DDX31 is a member of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region. Pssm-ID: 350707 [Multi-domain] Cd Length: 214 Bit Score: 143.50 E-value: 4.63e-39
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| DEADc_DDX52 | cd17957 | DEAD-box helicase domain of DEAD box protein 52; DDX52 (also called ROK1 and HUSSY19) is ... |
121-301 | 9.68e-39 | |||||||
DEAD-box helicase domain of DEAD box protein 52; DDX52 (also called ROK1 and HUSSY19) is ubiquitously expressed in testis, endometrium, and other tissues in humans. DDX52 is a member of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region. Pssm-ID: 350715 [Multi-domain] Cd Length: 198 Bit Score: 141.96 E-value: 9.68e-39
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| DEADc_EIF4AII_EIF4AI_DDX2 | cd18046 | DEAD-box helicase domain of eukaryotic initiation factor 4A-I and 4-II; Eukaryotic initiation ... |
122-301 | 1.03e-38 | |||||||
DEAD-box helicase domain of eukaryotic initiation factor 4A-I and 4-II; Eukaryotic initiation factor 4A-I (DDX2A) and eukaryotic initiation factor 4A-II (DDX2B) are involved in cap recognition and are required for mRNA binding to ribosome. They are DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region. Pssm-ID: 350804 [Multi-domain] Cd Length: 201 Bit Score: 142.20 E-value: 1.03e-38
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| DEADc_DDX55 | cd17960 | DEAD-box helicase domain of DEAD box protein 55; DDX55 is a member of the DEAD-box helicases, ... |
107-287 | 3.82e-38 | |||||||
DEAD-box helicase domain of DEAD box protein 55; DDX55 is a member of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region. Pssm-ID: 350718 [Multi-domain] Cd Length: 202 Bit Score: 140.40 E-value: 3.82e-38
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| DEADc_DDX17 | cd18050 | DEAD-box helicase domain of DEAD box protein 17; DDX17 (also called DEAD Box Protein P72 or ... |
121-309 | 7.88e-38 | |||||||
DEAD-box helicase domain of DEAD box protein 17; DDX17 (also called DEAD Box Protein P72 or DEAD Box Protein P82) has a wide variety of functions including regulating the alternative splicing of exons exhibiting specific features such as the inclusion of AC-rich alternative exons in CD44 transcripts, playing a role in innate immunity, and promoting mRNA degradation mediated by the antiviral zinc-finger protein ZC3HAV1 in an ATPase-dependent manner. DDX17 synergizes with DDX5 and SRA1 RNA to activate MYOD1 transcriptional activity and is involved in skeletal muscle differentiation. DDX17 is a member of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region. Pssm-ID: 350808 [Multi-domain] Cd Length: 271 Bit Score: 142.07 E-value: 7.88e-38
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| DEADc_DDX47 | cd17954 | DEAD-box helicase domain of DEAD box protein 47; DDX47 (also called E4-DEAD box protein) can ... |
121-287 | 2.48e-37 | |||||||
DEAD-box helicase domain of DEAD box protein 47; DDX47 (also called E4-DEAD box protein) can shuttle between the nucleus and the cytoplasm, and has an RNA-independent ATPase activity. DX47 is a member of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region. Pssm-ID: 350712 [Multi-domain] Cd Length: 203 Bit Score: 138.22 E-value: 2.48e-37
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| DEADc_DDX56 | cd17961 | DEAD-box helicase domain of DEAD box protein 56; DDX56 is a helicase required for assembly of ... |
121-287 | 1.09e-36 | |||||||
DEAD-box helicase domain of DEAD box protein 56; DDX56 is a helicase required for assembly of infectious West Nile virus particles. New research suggests that DDX56 relocalizes to the site of virus assembly during WNV infection and that its interaction with WNV capsid in the cytoplasm may occur transiently during virion morphogenesis. DDX56 is a member of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region. Pssm-ID: 350719 [Multi-domain] Cd Length: 206 Bit Score: 136.56 E-value: 1.09e-36
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| DEADc_DDX59 | cd17962 | DEAD-box helicase domain of DEAD box protein 59; DDX59 plays an important role in lung cancer ... |
111-301 | 1.40e-36 | |||||||
DEAD-box helicase domain of DEAD box protein 59; DDX59 plays an important role in lung cancer development by promoting DNA replication. DDX59 knockdown mice showed reduced cell proliferation, anchorage-independent cell growth, and reduction of tumor formation. Recent work shows that EGFR and Ras regulate DDX59 during lung cancer development. Diseases associated with DDX59 (also called zinc finger HIT domain-containing protein 5) include orofaciodigital syndrome V and orofaciodigital syndrome. DDX59 is a member of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region. Pssm-ID: 350720 [Multi-domain] Cd Length: 193 Bit Score: 135.75 E-value: 1.40e-36
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| DEADc_DDX41 | cd17951 | DEAD-box helicase domain of DEAD box protein 41; DDX41 (also called ABS and MPLPF) interacts ... |
108-297 | 6.52e-36 | |||||||
DEAD-box helicase domain of DEAD box protein 41; DDX41 (also called ABS and MPLPF) interacts with several spliceosomal proteins and may recognize the bacterial second messengers cyclic di-GMP and cyclic di-AMP, resulting in the induction of genes involved in the innate immune response. Diseases associated with DDX41 include "myeloproliferative/lymphoproliferative neoplasms, familial" and "Ddx41-related susceptibility to familial myeloproliferative/lymphoproliferative neoplasms". DDX41 is a member of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region. Pssm-ID: 350709 [Multi-domain] Cd Length: 206 Bit Score: 134.39 E-value: 6.52e-36
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| DEADc_DDX19_DDX25 | cd17963 | DEAD-box helicase domain of ATP-dependent RNA helicases DDX19 and DDX25; DDX19 (also called ... |
110-301 | 8.08e-36 | |||||||
DEAD-box helicase domain of ATP-dependent RNA helicases DDX19 and DDX25; DDX19 (also called DEAD box RNA helicase DEAD5) and DDX25 (also called gonadotropin-regulated testicular RNA helicase (GRTH)) are members of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region. Pssm-ID: 350721 [Multi-domain] Cd Length: 196 Bit Score: 133.85 E-value: 8.08e-36
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| DEADc_DDX49 | cd17955 | DEAD-box helicase domain of DEAD box protein 49; DDX49 (also called Dbp8) is a member of the ... |
98-287 | 9.70e-36 | |||||||
DEAD-box helicase domain of DEAD box protein 49; DDX49 (also called Dbp8) is a member of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region. Pssm-ID: 350713 [Multi-domain] Cd Length: 204 Bit Score: 133.89 E-value: 9.70e-36
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| DEADc_DDX18 | cd17942 | DEAD-box helicase domain of DEAD box protein 18; This DDX18 gene encodes a DEAD box protein ... |
107-287 | 1.27e-35 | |||||||
DEAD-box helicase domain of DEAD box protein 18; This DDX18 gene encodes a DEAD box protein and is activated by Myc protein. DDX18 is a member of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region. Pssm-ID: 350700 [Multi-domain] Cd Length: 198 Bit Score: 133.25 E-value: 1.27e-35
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| DEADc_DDX20 | cd17943 | DEAD-box helicase domain of DEAD box protein 20; DDX20 (also called DEAD Box Protein DP 103, ... |
107-302 | 2.79e-35 | |||||||
DEAD-box helicase domain of DEAD box protein 20; DDX20 (also called DEAD Box Protein DP 103, Component Of Gems 3, Gemin-3, and SMN-Interacting Protein) interacts directly with SMN (survival of motor neurons), the spinal muscular atrophy gene product, and may play a catalytic role in the function of the SMN complex on ribonucleoproteins. Diseases associated with DDX20 include spinal muscular atrophy and muscular atrophy. DDX20 is a member of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region. Pssm-ID: 350701 [Multi-domain] Cd Length: 192 Bit Score: 132.00 E-value: 2.79e-35
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| DEADc_DDX39 | cd17950 | DEAD-box helicase domain of DEAD box protein 39; DDX39A is involved in pre-mRNA splicing and ... |
98-305 | 4.90e-35 | |||||||
DEAD-box helicase domain of DEAD box protein 39; DDX39A is involved in pre-mRNA splicing and is required for the export of mRNA out of the nucleus. DDX39B is an essential splicing factor required for association of U2 small nuclear ribonucleoprotein with pre-mRNA, and it also plays an important role in mRNA export from the nucleus to the cytoplasm. Diseases associated with DDX39A (also called UAP56-Related Helicase, 49 kDa) include gastrointestinal stromal tumor and inflammatory bowel disease 6, while diseases associated with DDX39B (also called 56 kDa U2AF65-Associated Protein) include Plasmodium vivax malaria. DDX39 is a member of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region. Pssm-ID: 350708 [Multi-domain] Cd Length: 208 Bit Score: 132.08 E-value: 4.90e-35
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| DEADc_DDX3 | cd18051 | DEAD-box helicase domain of DEAD box protein 3; DDX3 (also called helicase-like protein, DEAD ... |
121-289 | 5.26e-35 | |||||||
DEAD-box helicase domain of DEAD box protein 3; DDX3 (also called helicase-like protein, DEAD box, X isoform, or DDX14) has been reported to display a high level of RNA-independent ATPase activity stimulated by both RNA and DNA. This protein has multiple conserved domains and is thought to play roles in both the nucleus and cytoplasm. Nuclear roles include transcriptional regulation, mRNP assembly, pre-mRNA splicing, and mRNA export. In the cytoplasm, this protein is thought to be involved in translation, cellular signaling, and viral replication. Misregulation of this gene has been implicated in tumorigenesis. Diseases associated with DDX3 include mental retardation, X-linked 102 and agenesis of the corpus callosum, with facial anomalies and robin sequence. DDX3 is a member of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region. Pssm-ID: 350809 [Multi-domain] Cd Length: 249 Bit Score: 133.24 E-value: 5.26e-35
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| DEADc_DDX42 | cd17952 | DEAD-box helicase domain of DEAD box protein 42; DDX42 (also called Splicing Factor ... |
121-287 | 5.54e-35 | |||||||
DEAD-box helicase domain of DEAD box protein 42; DDX42 (also called Splicing Factor 3B-Associated 125 kDa Protein, RHELP, or RNAHP) is an NTPase with a preference for ATP, the hydrolysis of which is enhanced by various RNA substrates. It acts as a non-processive RNA helicase with protein displacement and RNA annealing activities. DDX42 is a member of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region. Pssm-ID: 350710 [Multi-domain] Cd Length: 197 Bit Score: 131.38 E-value: 5.54e-35
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| Helicase_C | pfam00271 | Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ... |
332-442 | 1.89e-32 | |||||||
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: 121.16 E-value: 1.89e-32
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| DEADc_DDX24 | cd17946 | DEAD-box helicase domain of DEAD box protein 24; The human DDX24 gene encodes a DEAD box ... |
121-287 | 2.45e-32 | |||||||
DEAD-box helicase domain of DEAD box protein 24; The human DDX24 gene encodes a DEAD box protein, which shows little similarity to any of the other known human DEAD box proteins, but shows a high similarity to mouse Ddx24 at the amino acid level. MDM2 mediates nonproteolytic polyubiquitylation of the DEAD-Box RNA helicase DDX24. DDX24 is a member of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP- binding region. Pssm-ID: 350704 [Multi-domain] Cd Length: 235 Bit Score: 125.04 E-value: 2.45e-32
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| DEADc_DDX1 | cd17938 | DEAD-box helicase domain of DEAD box protein 1; DEAD box protein 1 (DDX1) acts as an ... |
121-287 | 3.68e-32 | |||||||
DEAD-box helicase domain of DEAD box protein 1; DEAD box protein 1 (DDX1) acts as an ATP-dependent RNA helicase, able to unwind both RNA-RNA and RNA-DNA duplexes. It possesses 5' single-stranded RNA overhang nuclease activity as well as ATPase activity on various RNA, but not DNA polynucleotides. DDX1 may play a role in RNA clearance at DNA double-strand breaks (DSBs), thereby facilitating the template-guided repair of transcriptionally active regions of the genome. It may also be involved in 3'-end cleavage and polyadenylation of pre-mRNAs. DDX1 is a member of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region. Pssm-ID: 350696 [Multi-domain] Cd Length: 204 Bit Score: 123.59 E-value: 3.68e-32
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| DEADc_EIF4AIII_DDX48 | cd18045 | DEAD-box helicase domain of eukaryotic initiation factor 4A-III; Eukaryotic initiation factor ... |
98-300 | 2.58e-31 | |||||||
DEAD-box helicase domain of eukaryotic initiation factor 4A-III; Eukaryotic initiation factor 4A-III (EIF4AIII, also known as DDX48) is part of the exon junction complex (EJC) that plays a major role in posttranscriptional regulation of mRNA. EJC consists of four proteins (eIF4AIII, Barentsz [Btz], Mago, and Y14), mRNA, and ATP. DDX48 is a member of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region. Pssm-ID: 350803 [Multi-domain] Cd Length: 201 Bit Score: 121.04 E-value: 2.58e-31
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| DEADc_DDX51 | cd17956 | DEAD-box helicase domain of DEAD box protein 51; DDX51 aids cell cancer proliferation by ... |
108-287 | 1.22e-29 | |||||||
DEAD-box helicase domain of DEAD box protein 51; DDX51 aids cell cancer proliferation by regulating multiple signalling pathways. Mammalian DEAD box protein Ddx51 acts in 3' end maturation of 28S rRNA by promoting the release of U8 snoRNA.It is a member of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region. Pssm-ID: 350714 [Multi-domain] Cd Length: 231 Bit Score: 117.35 E-value: 1.22e-29
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| DEADc_DDX28 | cd17948 | DEAD-box helicase domain of DEAD box protein 28; DDX28 (also called mitochondrial DEAD-box ... |
108-289 | 1.16e-26 | |||||||
DEAD-box helicase domain of DEAD box protein 28; DDX28 (also called mitochondrial DEAD-box polypeptide 28) plays an essential role in facilitating the proper assembly of the mitochondrial large ribosomal subunit and its helicase activity is essential for this function. DDX28 is a member of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region. Pssm-ID: 350706 [Multi-domain] Cd Length: 231 Bit Score: 108.61 E-value: 1.16e-26
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| HELICc | smart00490 | helicase superfamily c-terminal domain; |
376-442 | 7.03e-26 | |||||||
helicase superfamily c-terminal domain; Pssm-ID: 197757 [Multi-domain] Cd Length: 82 Bit Score: 101.52 E-value: 7.03e-26
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| SF2-N | cd00046 | N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ... |
133-287 | 1.59e-20 | |||||||
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: 88.23 E-value: 1.59e-20
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| YprA | COG1205 | ATP-dependent helicase YprA, contains C-terminal metal-binding DUF1998 domain [Replication, ... |
94-448 | 1.13e-19 | |||||||
ATP-dependent helicase YprA, contains C-terminal metal-binding DUF1998 domain [Replication, recombination and repair]; Pssm-ID: 440818 [Multi-domain] Cd Length: 758 Bit Score: 93.75 E-value: 1.13e-19
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| GUCT_RH7_like | cd12937 | RNA-binding GUCT domain found in plant DEAD-box ATP-dependent RNA helicase 7 (RH7) and similar ... |
537-622 | 3.34e-19 | |||||||
RNA-binding GUCT domain found in plant DEAD-box ATP-dependent RNA helicase 7 (RH7) and similar proteins; This subfamily corresponds to the Gu C-terminal (GUCT) domain of RH7 and similar proteins. RH7, also termed plant RNA helicase 75 (PRH75), is a new nucleus-localized member of the DEAD-box protein family from higher plants. It displays a weak ATPase activity which is barely stimulated by RNA ligands. RH7 contains an N-terminal KDES domain rich in lysine, glutamic acid, aspartic acid, and serine residues, seven highly conserved helicase motifs in the central region, a GUCT domain, and a C-terminal GYR domain harboring a large number of glycine residues interrupted by either arginines or tyrosines. RH7 is RNA specific and harbors two possible RNA-binding motifs, the helicase motif VI (HRIGRTGR) and the C-terminal glycine-rich GYR domain. Pssm-ID: 240594 Cd Length: 86 Bit Score: 82.61 E-value: 3.34e-19
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| SSL2 | COG1061 | Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair]; |
133-421 | 7.96e-18 | |||||||
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair]; Pssm-ID: 440681 [Multi-domain] Cd Length: 566 Bit Score: 87.39 E-value: 7.96e-18
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| DEADc_MRH4 | cd17965 | DEAD-box helicase domain of ATP-dependent RNA helicase MRH4; Mitochondrial RNA helicase 4 ... |
136-304 | 2.38e-17 | |||||||
DEAD-box helicase domain of ATP-dependent RNA helicase MRH4; Mitochondrial RNA helicase 4 (MRH4) plays an essential role during the late stages of mitochondrial ribosome or mitoribosome assembly by promoting remodeling of the 21S rRNA-protein interactions. MRH4 is a member of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region. Pssm-ID: 350723 [Multi-domain] Cd Length: 251 Bit Score: 82.04 E-value: 2.38e-17
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| DEADc_DDX25 | cd18048 | DEAD-box helicase domain of DEAD box protein 25; DDX25 (also called gonadotropin-regulated ... |
97-298 | 5.92e-16 | |||||||
DEAD-box helicase domain of DEAD box protein 25; DDX25 (also called gonadotropin-regulated testicular RNA helicase (GRTH) is a testis-specific protein essential for completion of spermatogenesis. DDX25 is also a novel negative regulator of IFN pathway and facilitates RNA virus infection. Diseases associated with DDX25 include hydrolethalus syndrome, an autosomal recessive lethal malformation syndrome characterized by multiple developmental defects of fetus.. DDX25 (also called gonadotropin-regulated testicular RNA helicase) is a member of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region. Pssm-ID: 350806 [Multi-domain] Cd Length: 229 Bit Score: 77.75 E-value: 5.92e-16
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| BRR2 | COG1204 | Replicative superfamily II helicase [Replication, recombination and repair]; |
105-445 | 1.40e-15 | |||||||
Replicative superfamily II helicase [Replication, recombination and repair]; Pssm-ID: 440817 [Multi-domain] Cd Length: 529 Bit Score: 79.94 E-value: 1.40e-15
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| SF2_C_RecQ | cd18794 | C-terminal helicase domain of the RecQ family helicases; The RecQ helicase family is an ... |
341-451 | 2.90e-15 | |||||||
C-terminal helicase domain of the RecQ family helicases; The RecQ helicase family is an evolutionarily conserved class of enzymes, dedicated to preserving genomic integrity by operating in telomere maintenance, DNA repair, and replication. They 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: 350181 [Multi-domain] Cd Length: 134 Bit Score: 73.01 E-value: 2.90e-15
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| PRK13766 | PRK13766 | Hef nuclease; Provisional |
383-539 | 1.97e-14 | |||||||
Hef nuclease; Provisional Pssm-ID: 237496 [Multi-domain] Cd Length: 773 Bit Score: 76.84 E-value: 1.97e-14
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| MPH1 | COG1111 | ERCC4-related helicase [Replication, recombination and repair]; |
383-442 | 1.44e-13 | |||||||
ERCC4-related helicase [Replication, recombination and repair]; Pssm-ID: 440728 [Multi-domain] Cd Length: 718 Bit Score: 74.00 E-value: 1.44e-13
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| DEXHc_Ski2 | cd17921 | DEXH-box helicase domain of DEAD-like helicase Ski2 family proteins; Ski2-like RNA helicases ... |
118-287 | 2.71e-13 | |||||||
DEXH-box helicase domain of DEAD-like helicase Ski2 family proteins; Ski2-like RNA helicases play an important role in RNA degradation, processing, and splicing pathways. They belong to the type II DEAD box helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350679 [Multi-domain] Cd Length: 181 Bit Score: 68.83 E-value: 2.71e-13
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| SF2_C_FANCM_Hef | cd18801 | C-terminal helicase domain of Fanconi anemia group M family helicases; Fanconi anemia group M ... |
350-440 | 3.39e-12 | |||||||
C-terminal helicase domain of Fanconi anemia group M family helicases; Fanconi anemia group M (FANCM) protein is a DNA-dependent ATPase component of the Fanconi anemia (FA) core complex. It is required for the normal activation of the FA pathway, leading to monoubiquitination of the FANCI-FANCD2 complex in response to DNA damage, cellular resistance to DNA cross-linking drugs, and prevention of chromosomal breakage. Hef (helicase-associated endonuclease fork-structure) belongs to the XPF/MUS81/FANCM family of endonucleases and is involved in stalled replication fork repair. FANCM and Hef 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: 350188 [Multi-domain] Cd Length: 143 Bit Score: 64.30 E-value: 3.39e-12
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| SF2_C_dicer | cd18802 | C-terminal helicase domain of the endoribonuclease Dicer; Dicer ribonucleases cleave ... |
350-441 | 8.27e-12 | |||||||
C-terminal helicase domain of the endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded RNA (dsRNA) precursors to generate microRNAs (miRNAs) and small interfering RNAs (siRNAs). In concert with Argonautes, these small RNAs bind complementary mRNAs to down-regulate their expression. miRNAs are processed by Dicer from small hairpins, while siRNAs are typically processed from longer dsRNA, from endogenous sources, or exogenous sources such as viral replication intermediates. Some organisms, such as Homo sapiens and Caenorhabditis elegans, encode one Dicer that generates miRNAs and siRNAs, but other organisms have multiple dicers with specialized functions. Dicer exists throughout eukaryotes, and a subset has an N-terminal helicase domain of the RIG-I-like receptor (RLR) subgroup. RLRs often function in innate immunity and Dicer helicase domains sometimes show differences in activity that correlate with roles in immunity. Dicer helicase domains 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: 350189 [Multi-domain] Cd Length: 142 Bit Score: 63.38 E-value: 8.27e-12
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| GUCT | cd12929 | RNA-binding GUCT domain found in the RNA helicase II/Gu protein family; This family includes ... |
545-618 | 2.44e-10 | |||||||
RNA-binding GUCT domain found in the RNA helicase II/Gu protein family; This family includes vertebrate RNA helicase II/Gualpha (RH-II/Gualpha) and RNA helicase II/Gubeta (RH-II/Gubeta), both of which consist of a DEAD box helicase domain (DEAD), a helicase conserved C-terminal domain, and a Gu C-terminal (GUCT) domain. They localize to nucleoli, suggesting roles in ribosomal RNA production, but RH-II/Gubeta also localizes to nuclear speckles containing the splicing factor SC35, suggesting its possible involvement in pre-mRNA splicing. In contrast to RH-II/Gualpha, RH-II/Gubeta has RNA-unwinding activity, but no RNA-folding activity. The family also contains plant DEAD-box ATP-dependent RNA helicase 7 (RH7 or PRH75), Thermus thermophilus heat resistant RNA-dependent ATPase (Hera) and similar proteins. RH7 is a new nucleus-localized member of the DEAD-box protein family from higher plants. It displays a weak ATPase activity which is barely stimulated by RNA ligands. RH7 contains an N-terminal KDES domain rich in lysine, glutamic acid, aspartic acid, and serine residues, seven highly conserved helicase motifs in the central region, a GUCT domain, and a C-terminal GYR domain harboring a large number of glycine residues interrupted by either arginines or tyrosines. Thermus thermophilus Hera is a DEAD box helicase that binds fragments of 23S rRNA and RNase P RNA via its C-terminal domain. It contains a helicase core that harbors two RecA-like domains termed RecA_N and RecA_C, a dimerization domain (DD), and a C-terminal RNA-binding domain (RBD) that reveals a compact, RRM-like fold and shows sequence similarity with the typical GUCT domain found in the RNA helicase II/Gu protein family. Pssm-ID: 240592 Cd Length: 72 Bit Score: 56.95 E-value: 2.44e-10
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| DEADc_DDX19 | cd18047 | DEAD-box helicase domain of DEAD box protein 19; DDX19 is an RNA helicase involved in both ... |
134-298 | 3.75e-10 | |||||||
DEAD-box helicase domain of DEAD box protein 19; DDX19 is an RNA helicase involved in both mRNA (mRNA) export from the nucleus into the cytoplasm and in mRNA translation. DDX19 functions in the nucleus in resolving RNA:DNA hybrids (R-loops). Activation of a DNA damage response pathway dependent upon the ATR kinase, a major regulator of replication fork progression, stimulates translocation of DDX19 from the cytoplasm into the nucleus. Only nuclear Ddx19 is competent to resolve R-loops. DDX19 is a member of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region. Pssm-ID: 350805 [Multi-domain] Cd Length: 205 Bit Score: 60.12 E-value: 3.75e-10
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| SF2_C_XPB | cd18789 | C-terminal helicase domain of XPB-like helicases; TFIIH basal transcription factor complex ... |
349-443 | 5.50e-10 | |||||||
C-terminal helicase domain of XPB-like helicases; TFIIH basal transcription factor complex helicase XPB (xeroderma pigmentosum type B) subunit (also known as DNA excision repair protein ERCC-3 or TFIIH 89 kDa subunit) is the ATP-dependent 3'-5' DNA helicase component of the core-TFIIH basal transcription factor, involved in nucleotide excision repair (NER) of DNA and, when complexed to CAK, in RNA transcription by RNA polymerase II. XPB is a DEAD-like helicase 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: 350176 [Multi-domain] Cd Length: 153 Bit Score: 58.41 E-value: 5.50e-10
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| SF2_C | cd18785 | C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases ... |
347-451 | 5.51e-10 | |||||||
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: 56.17 E-value: 5.51e-10
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| DEXHc_Hrq1-like | cd17923 | DEAH-box helicase domain of Hrq1 and similar proteins; Yeast Hrq1, similar to RecQ4, plays a ... |
123-250 | 9.46e-10 | |||||||
DEAH-box helicase domain of Hrq1 and similar proteins; Yeast Hrq1, similar to RecQ4, plays a role in DNA inter-strand crosslink (ICL) repair and in telomere maintenance. Hrq1 lacks the Sld2-like domain found in RecQ4. Hrq1 belongs to the type II DEAD box helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350681 [Multi-domain] Cd Length: 182 Bit Score: 58.37 E-value: 9.46e-10
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| COG1202 | COG1202 | Superfamily II helicase, archaea-specific [Replication, recombination and repair]; |
92-414 | 5.08e-09 | |||||||
Superfamily II helicase, archaea-specific [Replication, recombination and repair]; Pssm-ID: 440815 [Multi-domain] Cd Length: 790 Bit Score: 59.52 E-value: 5.08e-09
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| cas3_core | TIGR01587 | CRISPR-associated helicase Cas3; This model represents the highly conserved core region of an ... |
135-443 | 7.86e-09 | |||||||
CRISPR-associated helicase Cas3; This model represents the highly conserved core region of an alignment of Cas3, a protein found in association with CRISPR repeat elements in a broad range of bacteria and archaea. Cas3 appears to be a helicase, with regions found by pfam00270 (DEAD/DEAH box helicase) and pfam00271 (Helicase conserved C-terminal domain). Some but not all members have an N-terminal HD domain region (pfam01966) that is not included within this model. Pssm-ID: 273707 [Multi-domain] Cd Length: 359 Bit Score: 57.85 E-value: 7.86e-09
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| Cas3_I | cd09639 | CRISPR/Cas system-associated protein Cas3; CRISPR (Clustered Regularly Interspaced Short ... |
135-443 | 7.98e-09 | |||||||
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: 57.82 E-value: 7.98e-09
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| SF2_C_EcoAI-like | cd18799 | C-terminal helicase domain of EcoAI HsdR-like restriction enzyme family helicases; This family ... |
343-420 | 9.27e-09 | |||||||
C-terminal helicase domain of EcoAI HsdR-like restriction enzyme family helicases; This family is composed of helicase restriction enzymes, including the HsdR subunit of restriction-modification enzymes such as Escherichia coli type I restriction enzyme EcoAI R protein (R.EcoAI). The EcoAI enzyme recognizes 5'-GAGN(7)GTCA-3'. The HsdR or R subunit is required for both nuclease and ATPase activities, but not for modification. These proteins 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: 350186 [Multi-domain] Cd Length: 116 Bit Score: 53.72 E-value: 9.27e-09
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| Cas3 | COG1203 | CRISPR-Cas type I system-associated endonuclease/helicase Cas3 [Defense mechanisms]; ... |
119-443 | 1.47e-08 | |||||||
CRISPR-Cas type I system-associated endonuclease/helicase Cas3 [Defense mechanisms]; CRISPR-Cas type I system-associated endonuclease/helicase Cas3 is part of the Pathway/BioSystem: CRISPR-Cas system Pssm-ID: 440816 [Multi-domain] Cd Length: 535 Bit Score: 57.78 E-value: 1.47e-08
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| RecQ | COG0514 | Superfamily II DNA helicase RecQ [Replication, recombination and repair]; |
326-451 | 1.85e-08 | |||||||
Superfamily II DNA helicase RecQ [Replication, recombination and repair]; Pssm-ID: 440280 [Multi-domain] Cd Length: 489 Bit Score: 57.46 E-value: 1.85e-08
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| SF2_C_LHR | cd18796 | C-terminal helicase domain of LHR family helicases; Large helicase-related protein (LHR) is a ... |
378-440 | 2.27e-07 | |||||||
C-terminal helicase domain of LHR family helicases; Large helicase-related protein (LHR) is a DNA damage-inducible helicase that uses ATP hydrolysis to drive unidirectional 3'-to-5' translocation along single-stranded DNA (ssDNA) and to unwind RNA:DNA duplexes. This group also includes related bacterial and archaeal helicases. LHR family helicases 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: 350183 [Multi-domain] Cd Length: 150 Bit Score: 50.73 E-value: 2.27e-07
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| ResIII | pfam04851 | Type III restriction enzyme, res subunit; |
134-290 | 4.14e-07 | |||||||
Type III restriction enzyme, res subunit; Pssm-ID: 398492 [Multi-domain] Cd Length: 162 Bit Score: 50.36 E-value: 4.14e-07
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| DEXHc_dicer | cd18034 | DEXH-box helicase domain of endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded ... |
134-251 | 4.19e-07 | |||||||
DEXH-box helicase domain of endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded RNA (dsRNA) precursors to generate microRNAs (miRNAs) and small interfering RNAs (siRNAs). In concert with Argonautes, these small RNAs bind complementary mRNAs to down-regulate their expression. miRNAs are processed by Dicer from small hairpins, while siRNAs are typically processed from longer dsRNA, from endogenous sources, or exogenous sources such as viral replication intermediates. Some organisms, such as Homo sapiens and Caenorhabditis elegans, encode one Dicer that generates miRNAs and siRNAs, but other organisms have multiple dicers with specialized functions. Dicers exist throughout eukaryotes, and a subset have an N-terminal helicase domain of the RIG-I-like receptor (RLR) subgroup. RLRs often function in innate immunity and Dicer helicase domains sometimes show differences in activity that correlate with roles in immunity. Dicer 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: 350792 [Multi-domain] Cd Length: 200 Bit Score: 51.11 E-value: 4.19e-07
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| uvrb | TIGR00631 | excinuclease ABC, B subunit; All proteins in this family for wich functions are known are DNA ... |
341-453 | 5.21e-07 | |||||||
excinuclease ABC, B subunit; All proteins in this family for wich functions are known are DNA helicases that function in the nucleotide excision repair and are endonucleases that make the 3' incision next to DNA damage. They are part of a pathway requiring UvrA, UvrB, UvrC, and UvrD homologs. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University) [DNA metabolism, DNA replication, recombination, and repair] Pssm-ID: 273185 [Multi-domain] Cd Length: 655 Bit Score: 53.07 E-value: 5.21e-07
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| SF2_C_UvrB | cd18790 | C-terminal helicase domain of the UvrB family helicases; Excinuclease ABC subunit B (or UvrB) ... |
350-443 | 6.44e-07 | |||||||
C-terminal helicase domain of the UvrB family helicases; Excinuclease ABC subunit B (or UvrB) plays a central role in nucleotide excision repair (NER). Together with other components of the NER system, like UvrA, UvrC, UvrD (helicase II), and DNA polymerase I, it recognizes and cleaves damaged DNA in a multistep ATP-dependent reaction. UvrB is critical for the second phase of damage recognition by verifying the nature of the damage and forming the pre-incision complex. Its ATPase site becomes activated in the presence of UvrA and damaged DNA. Its activity is strand destabilization via distortion of the DNA at lesion site, with very limited DNA unwinding. UvrB is a DEAD-like helicase 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: 350177 [Multi-domain] Cd Length: 171 Bit Score: 49.94 E-value: 6.44e-07
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| SF2_C_Hrq | cd18797 | C-terminal helicase domain of HrQ family helicases; Yeast Hrq1, similar to RecQ4, plays a role ... |
350-443 | 1.09e-06 | |||||||
C-terminal helicase domain of HrQ family helicases; Yeast Hrq1, similar to RecQ4, plays a role in DNA inter-strand crosslink (ICL) repair and in telomere maintenance. Hrq1 lacks the Sld2-like domain found in RecQ4. HrQ family helicases 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: 350184 [Multi-domain] Cd Length: 146 Bit Score: 48.79 E-value: 1.09e-06
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| PRK09751 | PRK09751 | putative ATP-dependent helicase Lhr; Provisional |
374-439 | 1.66e-06 | |||||||
putative ATP-dependent helicase Lhr; Provisional Pssm-ID: 137505 [Multi-domain] Cd Length: 1490 Bit Score: 51.85 E-value: 1.66e-06
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| PRK00254 | PRK00254 | ski2-like helicase; Provisional |
102-251 | 3.14e-06 | |||||||
ski2-like helicase; Provisional Pssm-ID: 234702 [Multi-domain] Cd Length: 720 Bit Score: 50.59 E-value: 3.14e-06
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| PRK11057 | PRK11057 | ATP-dependent DNA helicase RecQ; Provisional |
340-451 | 2.10e-05 | |||||||
ATP-dependent DNA helicase RecQ; Provisional Pssm-ID: 182933 [Multi-domain] Cd Length: 607 Bit Score: 47.79 E-value: 2.10e-05
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| SF2_C_RecG_TRCF | cd18792 | C-terminal helicase domain of the RecG family helicases; The DEAD-like helicase RecG family ... |
377-455 | 2.52e-05 | |||||||
C-terminal helicase domain of the RecG family helicases; The DEAD-like helicase RecG family contains recombination factor RecG and transcription-repair coupling factor TrcF. They 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: 350179 [Multi-domain] Cd Length: 160 Bit Score: 44.95 E-value: 2.52e-05
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| PLN03137 | PLN03137 | ATP-dependent DNA helicase; Q4-like; Provisional |
352-451 | 3.37e-05 | |||||||
ATP-dependent DNA helicase; Q4-like; Provisional Pssm-ID: 215597 [Multi-domain] Cd Length: 1195 Bit Score: 47.20 E-value: 3.37e-05
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| HsdR | COG4096 | Type I site-specific restriction endonuclease, part of a restriction-modification system ... |
136-192 | 4.76e-05 | |||||||
Type I site-specific restriction endonuclease, part of a restriction-modification system [Defense mechanisms]; Pssm-ID: 443272 [Multi-domain] Cd Length: 806 Bit Score: 46.76 E-value: 4.76e-05
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| DEXHc_archSki2 | cd18028 | DEXH-box helicase domain of archaeal Ski2-type helicase; Archaeal Ski2-type RNA helicases play ... |
119-289 | 1.12e-04 | |||||||
DEXH-box helicase domain of archaeal Ski2-type helicase; Archaeal Ski2-type RNA helicases play an important role in RNA degradation, processing and splicing pathways. They belong to the type II DEAD box helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350786 [Multi-domain] Cd Length: 177 Bit Score: 43.48 E-value: 1.12e-04
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| DEXHc_RE | cd17926 | DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family ... |
142-287 | 1.17e-04 | |||||||
DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family is composed of helicase restriction enzymes and similar proteins such as TFIIH basal transcription factor complex helicase XPB subunit. These proteins are 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: 350684 [Multi-domain] Cd Length: 146 Bit Score: 42.68 E-value: 1.17e-04
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| UvrB | COG0556 | Excinuclease UvrABC helicase subunit UvrB [Replication, recombination and repair]; |
357-419 | 1.49e-04 | |||||||
Excinuclease UvrABC helicase subunit UvrB [Replication, recombination and repair]; Pssm-ID: 440322 [Multi-domain] Cd Length: 657 Bit Score: 45.00 E-value: 1.49e-04
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| SF2_C_TRCF | cd18810 | C-terminal helicase domain of the transcription-repair coupling factor; Transcription-repair ... |
377-455 | 1.51e-04 | |||||||
C-terminal helicase domain of the transcription-repair coupling factor; Transcription-repair coupling factor (TrcF) dissociates transcription elongation complexes blocked at nonpairing lesions and mediates recruitment of DNA repair proteins. TrcF is a DEAD-like helicase 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: 350197 [Multi-domain] Cd Length: 151 Bit Score: 42.72 E-value: 1.51e-04
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| DEXHc_RecG | cd17918 | DEXH/Q-box helicase domain of DEAD-like helicase RecG family proteins; The DEAD-like helicase ... |
135-250 | 1.58e-04 | |||||||
DEXH/Q-box helicase domain of DEAD-like helicase RecG family proteins; The DEAD-like helicase RecG family is part of the DEAD-like helicases superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350676 [Multi-domain] Cd Length: 180 Bit Score: 43.17 E-value: 1.58e-04
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| PRK05298 | PRK05298 | excinuclease ABC subunit UvrB; |
357-419 | 2.20e-04 | |||||||
excinuclease ABC subunit UvrB; Pssm-ID: 235395 [Multi-domain] Cd Length: 652 Bit Score: 44.65 E-value: 2.20e-04
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| DEXHc_Hef | cd18035 | DEXH-box helicase domain of Hef; Hef (helicase-associated endonuclease fork-structure) belongs ... |
133-250 | 2.41e-04 | |||||||
DEXH-box helicase domain of Hef; Hef (helicase-associated endonuclease fork-structure) belongs to the XPF/MUS81/FANCM family of endonucleases and is involved in stalled replication fork repair. All archaea encode a protein of the XPF/MUS81/FANCM family of endonucleases. It exists in two forms: a long form, referred as Hef which consists of an N-terminal helicase fused to a C-terminal nuclease and is specific to euryarchaea and a short form, referred as XPF which lacks the helicase domain and is specific to crenarchaea and thaumarchaea. Hef has the unique feature of having both active helicase and nuclease domains. This domain configuration is highly similar with the human FANCM, a possible ortholog of archaeal Hef proteins. Hef 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: 350793 [Multi-domain] Cd Length: 181 Bit Score: 42.50 E-value: 2.41e-04
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| SF2_C_RecG | cd18811 | C-terminal helicase domain of DNA helicase RecG; ATP-dependent DNA helicase RecG plays a ... |
377-454 | 2.52e-04 | |||||||
C-terminal helicase domain of DNA helicase RecG; ATP-dependent DNA helicase RecG plays a critical role in recombination and DNA repair. RecG helps process Holliday junction intermediates to mature products by catalyzing branch migration. It is a DEAD-like helicase 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: 350198 [Multi-domain] Cd Length: 159 Bit Score: 41.95 E-value: 2.52e-04
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| SF2_C_Ski2 | cd18795 | C-terminal helicase domain of the Ski2 family helicases; Ski2-like RNA helicases play an ... |
340-445 | 4.84e-04 | |||||||
C-terminal helicase domain of the Ski2 family helicases; Ski2-like RNA helicases play an important role in RNA degradation, processing, and splicing pathways. This family includes spliceosomal Brr2 RNA helicase, ASCC3 (involved in the repair of N-alkylated nucleotides), Mtr4 (involved in processing of structured RNAs), DDX60 (involved in viral RNA degradation), and other proteins. Ski2-like RNA helicases 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: 350182 [Multi-domain] Cd Length: 154 Bit Score: 41.00 E-value: 4.84e-04
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| DDXDc_reverse_gyrase | cd17924 | DDXD-box helicase domain of reverse gyrase; Reverse gyrase modifies the topological state of ... |
359-405 | 7.80e-04 | |||||||
DDXD-box helicase domain of reverse gyrase; Reverse gyrase modifies the topological state of DNA by introducing positive supercoils in an ATP-dependent process. Reverse gyrase belongs to the type II DEAD box helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350682 [Multi-domain] Cd Length: 189 Bit Score: 41.16 E-value: 7.80e-04
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| DEXHc_RIG-I | cd17927 | DEXH-box helicase domain of DEAD-like helicase RIG-I family proteins; Members of the RIG-I ... |
133-250 | 8.19e-04 | |||||||
DEXH-box helicase domain of DEAD-like helicase RIG-I family proteins; Members of the RIG-I family include FANCM, dicer, Hef, and the RIG-I-like receptors. Fanconi anemia group M (FANCM) protein is a DNA-dependent ATPase component of the Fanconi anemia (FA) core complex required for the normal activation of the FA pathway, leading to monoubiquitination of the FANCI-FANCD2 complex in response to DNA damage, cellular resistance to DNA cross-linking drugs, and prevention of chromosomal breakage. Dicer ribonucleases cleave double-stranded RNA (dsRNA) precursors to generate microRNAs (miRNAs) and small interfering RNAs (siRNAs). Hef (helicase-associated endonuclease fork-structure) is involved in stalled replication fork repair. RIG-I-like receptors (RLRs) sense cytoplasmic viral RNA and comprises RIG-I, RLR-2/MDA5 (melanoma differentiation-associated protein 5) and RLR-3/LGP2 (laboratory of genetics and physiology 2). The RIG-I family 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: 350685 [Multi-domain] Cd Length: 201 Bit Score: 41.26 E-value: 8.19e-04
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| DEXHc_LHR-like | cd17922 | DEXH-box helicase domain of LHR; Large helicase-related protein (LHR) is a DNA ... |
133-256 | 1.28e-03 | |||||||
DEXH-box helicase domain of LHR; Large helicase-related protein (LHR) is a DNA damage-inducible helicase that uses ATP hydrolysis to drive unidirectional 3'-to-5' translocation along single-stranded DNA (ssDNA) and to unwind RNA:DNA duplexes. This group also includes related bacterial and archaeal helicases from 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: 350680 [Multi-domain] Cd Length: 166 Bit Score: 40.26 E-value: 1.28e-03
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| SF2_C_reverse_gyrase | cd18798 | C-terminal helicase domain of the reverse gyrase; Reverse gyrase modifies the topological ... |
390-455 | 1.50e-03 | |||||||
C-terminal helicase domain of the reverse gyrase; Reverse gyrase modifies the topological state of DNA by introducing positive supercoils in an ATP-dependent process. Reverse gyrase is a DEAD-like helicase 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: 350185 [Multi-domain] Cd Length: 174 Bit Score: 39.98 E-value: 1.50e-03
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| CMS1 | pfam14617 | U3-containing 90S pre-ribosomal complex subunit; This is a family of fungal and plant ... |
216-249 | 1.55e-03 | |||||||
U3-containing 90S pre-ribosomal complex subunit; This is a family of fungal and plant CMS1-like proteins. The family has similarity to the DEAD-box helicases. Pssm-ID: 373164 Cd Length: 250 Bit Score: 41.00 E-value: 1.55e-03
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| GUCT_Hera | cd12938 | RNA-binding GUCT-like domain found in Thermus thermophilus heat resistant RNA-dependent ATPase ... |
536-606 | 1.68e-03 | |||||||
RNA-binding GUCT-like domain found in Thermus thermophilus heat resistant RNA-dependent ATPase (Hera) and similar proteins; This subfamily corresponds to the Gu C-terminal (GUCT)-like domain of Hera and similar proteins. Thermus thermophilus Hera is a DEAD box helicase that binds fragments of 23S rRNA and RNase P RNA via its C-terminal domain. It contains a helicase core that harbors two RecA-like domains termed RecA_N and RecA_C, a dimerization domain (DD), and a C-terminal RNA-binding domain (RBD) that reveals a compact, RRM-like fold and shows sequence similarity with GUCT domain found in vertebrate RNA helicase II/Gualpha (RH-II/Gualpha), RNA helicase II/Gubeta (RH-II/Gubeta) and plant DEAD-box ATP-dependent RNA helicase 7 (RH7 or PRH75). Pssm-ID: 240595 Cd Length: 74 Bit Score: 37.66 E-value: 1.68e-03
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| DEAD-like_helicase_C | cd09300 | C-terminal helicase domain of the DEAD-like helicases; This hierarchy of DEAD-like helicases ... |
400-445 | 1.83e-03 | |||||||
C-terminal helicase domain of the DEAD-like helicases; This hierarchy of DEAD-like helicases is composed of two superfamilies, SF1 and SF2, that share almost identical folds and extensive structural similarity in their catalytic core. Helicases are involved in ATP-dependent RNA or DNA unwinding. Two distinct types of helicases exist, those forming toroidal, predominantly hexameric structures, and those that do not. SF1 and SF2 helicases do not form toroidal structures, while SF3-6 helicases do. Their conserved 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: 350171 [Multi-domain] Cd Length: 59 Bit Score: 37.14 E-value: 1.83e-03
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| SF2_C_RHA | cd18791 | C-terminal helicase domain of the RNA helicase A (RHA) family helicases; The RNA helicase A ... |
377-451 | 1.94e-03 | |||||||
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: 39.82 E-value: 1.94e-03
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| DinG | COG1199 | Rad3-related DNA helicase DinG [Replication, recombination and repair]; |
124-197 | 1.95e-03 | |||||||
Rad3-related DNA helicase DinG [Replication, recombination and repair]; Pssm-ID: 440812 [Multi-domain] Cd Length: 629 Bit Score: 41.45 E-value: 1.95e-03
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| DEXHc_RE_I_III_res | cd18032 | DEXH-box helicase domain of type III restriction enzyme res subunit; Members of this model ... |
136-198 | 2.28e-03 | |||||||
DEXH-box helicase domain of type III restriction enzyme res subunit; Members of this model includes both type I and type III restriction enzymes. Both are hetero-oligomeric proteins. Type I REs are encoded by three closely linked genes: a specificity subunit (HsdS or S) for recognizing a DNA sequence, a methylation subunit (HsdM or M) for methylating the recognized target bases, and a restriction subunit (HsdR or R) for the translocation and random cleavage of non-methylated DNA. They show diverse catalytic activities, including methyltransferase (MTase), ATP hydrolase (ATPase), DNA translocation and restriction activities. These enzymes cut at a site that differs, and is a random distance (at least 1000 bp) away, from their recognition site. Cleavage at these random sites follows a process of DNA translocation, which shows that these enzymes are also molecular motors. The recognition site is asymmetrical and is composed of two specific portions: one containing 3-4 nucleotides, and another containing 4-5 nucleotides, separated by a non-specific spacer of about 6-8 nucleotides. Type III enzymes are composed of two subunits, Res and Mod. The Mod subunit recognizes the DNA sequence specific for the system and is a modification methyltransferase; as such, it is functionally equivalent to the M and S subunits of type I restriction endonucleases. Res is required for restriction, although it has no enzymatic activity on its own. Type III enzymes recognize short 5-6 bp-long asymmetric DNA sequences and cleave 25-27 bp downstream to leave short, single-stranded 5' protrusions. They require the presence of two inversely oriented unmethylated recognition sites for restriction to occur. These enzymes methylate only one strand of the DNA, at the N-6 position of adenosyl residues, so newly replicated DNA will have only one strand methylated, which is sufficient to protect against restriction. Both type I and type III REs are members 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: 350790 [Multi-domain] Cd Length: 163 Bit Score: 39.47 E-value: 2.28e-03
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| PTZ00146 | PTZ00146 | fibrillarin; Provisional |
632-678 | 4.39e-03 | |||||||
fibrillarin; Provisional Pssm-ID: 240291 Cd Length: 293 Bit Score: 39.72 E-value: 4.39e-03
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| DEXDc_ComFA | cd17925 | DEXD-box helicase domain of ComFA; ATP-dependent helicase ComFA (also called ComF operon ... |
130-287 | 4.63e-03 | |||||||
DEXD-box helicase domain of ComFA; ATP-dependent helicase ComFA (also called ComF operon protein 1) is part of the complex mediating the binding and uptake of single-stranded DNA. ComFA is required for DNA uptake but not for binding. It belongs to the type II DEAD box helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350683 [Multi-domain] Cd Length: 143 Bit Score: 38.05 E-value: 4.63e-03
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| PTZ00146 | PTZ00146 | fibrillarin; Provisional |
630-678 | 9.12e-03 | |||||||
fibrillarin; Provisional Pssm-ID: 240291 Cd Length: 293 Bit Score: 38.56 E-value: 9.12e-03
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| PTZ00146 | PTZ00146 | fibrillarin; Provisional |
633-680 | 9.53e-03 | |||||||
fibrillarin; Provisional Pssm-ID: 240291 Cd Length: 293 Bit Score: 38.56 E-value: 9.53e-03
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