DEAD box helicase [Ectocarpus siliculosus]
Protein Classification
List of domain hits
| Name | Accession | Description | Interval | E-value | ||||
| DEADc_DDX39 | cd17950 | DEAD-box helicase domain of DEAD box protein 39; DDX39A is involved in pre-mRNA splicing and ... |
58-266 | 6.26e-140 | ||||
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: 413.28 E-value: 6.26e-140
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| SF2_C_DEAD | cd18787 | C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse ... |
277-398 | 5.41e-40 | ||||
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: 143.80 E-value: 5.41e-40
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| PDI_a_family | cd02961 | Protein Disulfide Isomerase (PDIa) family, redox active TRX domains; composed of eukaryotic ... |
552-653 | 1.99e-30 | ||||
Protein Disulfide Isomerase (PDIa) family, redox active TRX domains; composed of eukaryotic proteins involved in oxidative protein folding in the endoplasmic reticulum (ER) by acting as catalysts and folding assistants. Members of this family include PDI and PDI-related proteins like ERp72, ERp57 (or ERp60), ERp44, P5, PDIR, ERp46 and the transmembrane PDIs. PDI, ERp57, ERp72, P5, PDIR and ERp46 are all oxidases, catalyzing the formation of disulfide bonds of newly synthesized polypeptides in the ER. They also exhibit reductase activity in acting as isomerases to correct any non-native disulfide bonds, as well as chaperone activity to prevent protein aggregation and facilitate the folding of newly synthesized proteins. These proteins usually contain multiple copies of a redox active TRX (a) domain containing a CXXC motif, and may also contain one or more redox inactive TRX-like (b) domains. Only one a domain is required for the oxidase function but multiple copies are necessary for the isomerase function. The different types of PDIs may show different substrate specificities and tissue-specific expression, or may be induced by stress. PDIs are in their reduced form at steady state and are oxidized to the active form by Ero1, which is localized in the ER through ERp44. Some members of this family also contain a DnaJ domain in addition to the redox active a domains; examples are ERdj5 and Pfj2. Also included in the family is the redox inactive N-terminal TRX-like domain of ERp29. : Pssm-ID: 239259 [Multi-domain] Cd Length: 101 Bit Score: 115.40 E-value: 1.99e-30
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| ERGIC_N | pfam13850 | Endoplasmic Reticulum-Golgi Intermediate Compartment (ERGIC); This family is the N-terminal of ... |
409-498 | 1.45e-29 | ||||
Endoplasmic Reticulum-Golgi Intermediate Compartment (ERGIC); This family is the N-terminal of ERGIC proteins, ER-Golgi intermediate compartment clusters, otherwise known as Ervs, and is associated with family COPIIcoated_ERV, pfam07970. : Pssm-ID: 464000 Cd Length: 91 Bit Score: 112.55 E-value: 1.45e-29
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| COPIIcoated_ERV super family | cl06835 | Endoplasmic reticulum vesicle transporter; This family is conserved from plants and fungi to ... |
684-850 | 1.24e-26 | ||||
Endoplasmic reticulum vesicle transporter; This family is conserved from plants and fungi to humans. Erv46 works in close conjunction with Erv41 and together they form a complex which cycles between the endoplasmic reticulum and Golgi complex. Erv46-41 interacts strongly with the endoplasmic reticulum glucosidase II. Mammalian glucosidase II comprises a catalytic alpha-subunit and a 58 kDa beta subunit, which is required for ER localization. All proteins identified biochemically as Erv41p-Erv46p interactors are localized to the early secretory pathway and are involved in protein maturation and processing in the ER and/or sorting into COPII vesicles for transport to the Golgi. The actual alignment was detected with superfamily member pfam07970: Pssm-ID: 462327 Cd Length: 225 Bit Score: 108.85 E-value: 1.24e-26
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| Name | Accession | Description | Interval | E-value | ||||||
| DEADc_DDX39 | cd17950 | DEAD-box helicase domain of DEAD box protein 39; DDX39A is involved in pre-mRNA splicing and ... |
58-266 | 6.26e-140 | ||||||
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: 413.28 E-value: 6.26e-140
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| SrmB | COG0513 | Superfamily II DNA and RNA helicase [Replication, recombination and repair]; |
61-398 | 5.98e-106 | ||||||
Superfamily II DNA and RNA helicase [Replication, recombination and repair]; Pssm-ID: 440279 [Multi-domain] Cd Length: 420 Bit Score: 333.27 E-value: 5.98e-106
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| PRK11776 | PRK11776 | ATP-dependent RNA helicase DbpA; Provisional |
66-398 | 8.53e-62 | ||||||
ATP-dependent RNA helicase DbpA; Provisional Pssm-ID: 236977 [Multi-domain] Cd Length: 460 Bit Score: 216.21 E-value: 8.53e-62
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| DEAD | pfam00270 | DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ... |
83-250 | 5.34e-44 | ||||||
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: 156.63 E-value: 5.34e-44
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| DEXDc | smart00487 | DEAD-like helicases superfamily; |
78-280 | 3.44e-43 | ||||||
DEAD-like helicases superfamily; Pssm-ID: 214692 [Multi-domain] Cd Length: 201 Bit Score: 155.73 E-value: 3.44e-43
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| SF2_C_DEAD | cd18787 | C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse ... |
277-398 | 5.41e-40 | ||||||
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: 143.80 E-value: 5.41e-40
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| PDI_a_family | cd02961 | Protein Disulfide Isomerase (PDIa) family, redox active TRX domains; composed of eukaryotic ... |
552-653 | 1.99e-30 | ||||||
Protein Disulfide Isomerase (PDIa) family, redox active TRX domains; composed of eukaryotic proteins involved in oxidative protein folding in the endoplasmic reticulum (ER) by acting as catalysts and folding assistants. Members of this family include PDI and PDI-related proteins like ERp72, ERp57 (or ERp60), ERp44, P5, PDIR, ERp46 and the transmembrane PDIs. PDI, ERp57, ERp72, P5, PDIR and ERp46 are all oxidases, catalyzing the formation of disulfide bonds of newly synthesized polypeptides in the ER. They also exhibit reductase activity in acting as isomerases to correct any non-native disulfide bonds, as well as chaperone activity to prevent protein aggregation and facilitate the folding of newly synthesized proteins. These proteins usually contain multiple copies of a redox active TRX (a) domain containing a CXXC motif, and may also contain one or more redox inactive TRX-like (b) domains. Only one a domain is required for the oxidase function but multiple copies are necessary for the isomerase function. The different types of PDIs may show different substrate specificities and tissue-specific expression, or may be induced by stress. PDIs are in their reduced form at steady state and are oxidized to the active form by Ero1, which is localized in the ER through ERp44. Some members of this family also contain a DnaJ domain in addition to the redox active a domains; examples are ERdj5 and Pfj2. Also included in the family is the redox inactive N-terminal TRX-like domain of ERp29. Pssm-ID: 239259 [Multi-domain] Cd Length: 101 Bit Score: 115.40 E-value: 1.99e-30
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| ERGIC_N | pfam13850 | Endoplasmic Reticulum-Golgi Intermediate Compartment (ERGIC); This family is the N-terminal of ... |
409-498 | 1.45e-29 | ||||||
Endoplasmic Reticulum-Golgi Intermediate Compartment (ERGIC); This family is the N-terminal of ERGIC proteins, ER-Golgi intermediate compartment clusters, otherwise known as Ervs, and is associated with family COPIIcoated_ERV, pfam07970. Pssm-ID: 464000 Cd Length: 91 Bit Score: 112.55 E-value: 1.45e-29
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| COPIIcoated_ERV | pfam07970 | Endoplasmic reticulum vesicle transporter; This family is conserved from plants and fungi to ... |
684-850 | 1.24e-26 | ||||||
Endoplasmic reticulum vesicle transporter; This family is conserved from plants and fungi to humans. Erv46 works in close conjunction with Erv41 and together they form a complex which cycles between the endoplasmic reticulum and Golgi complex. Erv46-41 interacts strongly with the endoplasmic reticulum glucosidase II. Mammalian glucosidase II comprises a catalytic alpha-subunit and a 58 kDa beta subunit, which is required for ER localization. All proteins identified biochemically as Erv41p-Erv46p interactors are localized to the early secretory pathway and are involved in protein maturation and processing in the ER and/or sorting into COPII vesicles for transport to the Golgi. Pssm-ID: 462327 Cd Length: 225 Bit Score: 108.85 E-value: 1.24e-26
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| Helicase_C | pfam00271 | Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ... |
303-398 | 1.80e-26 | ||||||
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: 104.21 E-value: 1.80e-26
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| ER_PDI_fam | TIGR01130 | protein disulfide isomerase, eukaryotic; This model represents eukaryotic protein disulfide ... |
549-657 | 3.26e-25 | ||||||
protein disulfide isomerase, eukaryotic; This model represents eukaryotic protein disulfide isomerases retained in the endoplasmic reticulum (ER) and closely related forms. Some members have been assigned alternative or additional functions such as prolyl 4-hydroxylase and dolichyl-diphosphooligosaccharide-protein glycotransferase. Members of this family have at least two protein-disulfide domains, each similar to thioredoxin but with the redox-active disulfide in the motif PWCGHCK, and an ER retention signal at the extreme C-terminus (KDEL, HDEL, and similar motifs). Pssm-ID: 273457 [Multi-domain] Cd Length: 462 Bit Score: 110.15 E-value: 3.26e-25
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| HELICc | smart00490 | helicase superfamily c-terminal domain; |
317-398 | 1.39e-23 | ||||||
helicase superfamily c-terminal domain; Pssm-ID: 197757 [Multi-domain] Cd Length: 82 Bit Score: 94.97 E-value: 1.39e-23
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| PTZ00102 | PTZ00102 | disulphide isomerase; Provisional |
549-653 | 1.37e-19 | ||||||
disulphide isomerase; Provisional Pssm-ID: 240266 [Multi-domain] Cd Length: 477 Bit Score: 92.89 E-value: 1.37e-19
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| Thioredoxin | pfam00085 | Thioredoxin; Thioredoxins are small enzymes that participate in redox reactions, via the ... |
551-653 | 3.99e-16 | ||||||
Thioredoxin; Thioredoxins are small enzymes that participate in redox reactions, via the reversible oxidation of an active centre disulfide bond. Some members with only the active site are not separated from the noise. Pssm-ID: 395038 [Multi-domain] Cd Length: 103 Bit Score: 74.58 E-value: 3.99e-16
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| CnoX | COG3118 | Chaperedoxin CnoX, contains thioredoxin-like and TPR-like domains, YbbN/TrxSC family ... |
553-630 | 1.81e-15 | ||||||
Chaperedoxin CnoX, contains thioredoxin-like and TPR-like domains, YbbN/TrxSC family [Posttranslational modification, protein turnover, chaperones]; Pssm-ID: 442352 [Multi-domain] Cd Length: 105 Bit Score: 72.93 E-value: 1.81e-15
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| RecQ | COG0514 | Superfamily II DNA helicase RecQ [Replication, recombination and repair]; |
306-398 | 4.52e-07 | ||||||
Superfamily II DNA helicase RecQ [Replication, recombination and repair]; Pssm-ID: 440280 [Multi-domain] Cd Length: 489 Bit Score: 53.22 E-value: 4.52e-07
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| cas3_core | TIGR01587 | CRISPR-associated helicase Cas3; This model represents the highly conserved core region of an ... |
238-398 | 5.10e-05 | ||||||
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: 46.29 E-value: 5.10e-05
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| PRK09751 | PRK09751 | putative ATP-dependent helicase Lhr; Provisional |
333-427 | 3.03e-03 | ||||||
putative ATP-dependent helicase Lhr; Provisional Pssm-ID: 137505 [Multi-domain] Cd Length: 1490 Bit Score: 41.45 E-value: 3.03e-03
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| Name | Accession | Description | Interval | E-value | ||||||
| DEADc_DDX39 | cd17950 | DEAD-box helicase domain of DEAD box protein 39; DDX39A is involved in pre-mRNA splicing and ... |
58-266 | 6.26e-140 | ||||||
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: 413.28 E-value: 6.26e-140
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| SrmB | COG0513 | Superfamily II DNA and RNA helicase [Replication, recombination and repair]; |
61-398 | 5.98e-106 | ||||||
Superfamily II DNA and RNA helicase [Replication, recombination and repair]; Pssm-ID: 440279 [Multi-domain] Cd Length: 420 Bit Score: 333.27 E-value: 5.98e-106
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| DEADc | cd00268 | DEAD-box helicase domain of DEAD box helicases; DEAD-box helicases comprise a diverse family ... |
70-264 | 6.26e-72 | ||||||
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: 234.64 E-value: 6.26e-72
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| PRK11776 | PRK11776 | ATP-dependent RNA helicase DbpA; Provisional |
66-398 | 8.53e-62 | ||||||
ATP-dependent RNA helicase DbpA; Provisional Pssm-ID: 236977 [Multi-domain] Cd Length: 460 Bit Score: 216.21 E-value: 8.53e-62
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| PTZ00424 | PTZ00424 | helicase 45; Provisional |
61-398 | 2.88e-60 | ||||||
helicase 45; Provisional Pssm-ID: 185609 [Multi-domain] Cd Length: 401 Bit Score: 210.45 E-value: 2.88e-60
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| PTZ00110 | PTZ00110 | helicase; Provisional |
54-398 | 1.99e-58 | ||||||
helicase; Provisional Pssm-ID: 240273 [Multi-domain] Cd Length: 545 Bit Score: 209.24 E-value: 1.99e-58
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| PRK11634 | PRK11634 | ATP-dependent RNA helicase DeaD; Provisional |
61-398 | 3.23e-58 | ||||||
ATP-dependent RNA helicase DeaD; Provisional Pssm-ID: 236941 [Multi-domain] Cd Length: 629 Bit Score: 210.47 E-value: 3.23e-58
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| PRK11192 | PRK11192 | ATP-dependent RNA helicase SrmB; Provisional |
61-398 | 5.81e-56 | ||||||
ATP-dependent RNA helicase SrmB; Provisional Pssm-ID: 236877 [Multi-domain] Cd Length: 434 Bit Score: 199.40 E-value: 5.81e-56
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| DEADc_DDX20 | cd17943 | DEAD-box helicase domain of DEAD box protein 20; DDX20 (also called DEAD Box Protein DP 103, ... |
70-244 | 2.71e-50 | ||||||
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: 175.14 E-value: 2.71e-50
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| PRK01297 | PRK01297 | ATP-dependent RNA helicase RhlB; Provisional |
58-398 | 8.96e-50 | ||||||
ATP-dependent RNA helicase RhlB; Provisional Pssm-ID: 234938 [Multi-domain] Cd Length: 475 Bit Score: 182.80 E-value: 8.96e-50
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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 ... |
61-264 | 1.45e-49 | ||||||
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: 173.64 E-value: 1.45e-49
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| DEADc_EIF4A | cd17939 | DEAD-box helicase domain of eukaryotic initiation factor 4A; The eukaryotic initiation ... |
63-264 | 1.70e-49 | ||||||
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: 173.28 E-value: 1.70e-49
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| PRK10590 | PRK10590 | ATP-dependent RNA helicase RhlE; Provisional |
66-398 | 2.35e-46 | ||||||
ATP-dependent RNA helicase RhlE; Provisional Pssm-ID: 236722 [Multi-domain] Cd Length: 456 Bit Score: 172.69 E-value: 2.35e-46
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| DEAD | pfam00270 | DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ... |
83-250 | 5.34e-44 | ||||||
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: 156.63 E-value: 5.34e-44
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| DEADc_MSS116 | cd17964 | DEAD-box helicase domain of DEAD-box helicase Mss116; Mss116 is an RNA chaperone important for ... |
66-255 | 9.54e-44 | ||||||
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: 157.36 E-value: 9.54e-44
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| DEADc_EIF4AII_EIF4AI_DDX2 | cd18046 | DEAD-box helicase domain of eukaryotic initiation factor 4A-I and 4-II; Eukaryotic initiation ... |
61-264 | 1.31e-43 | ||||||
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: 156.84 E-value: 1.31e-43
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| DEADc_DDX27 | cd17947 | DEAD-box helicase domain of DEAD box protein 27; DDX27 (also called RHLP, deficiency of ... |
70-249 | 2.51e-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: 155.88 E-value: 2.51e-43
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| DEXDc | smart00487 | DEAD-like helicases superfamily; |
78-280 | 3.44e-43 | ||||||
DEAD-like helicases superfamily; Pssm-ID: 214692 [Multi-domain] Cd Length: 201 Bit Score: 155.73 E-value: 3.44e-43
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| DEADc_DDX1 | cd17938 | DEAD-box helicase domain of DEAD box protein 1; DEAD box protein 1 (DDX1) acts as an ... |
61-258 | 1.68e-41 | ||||||
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: 150.93 E-value: 1.68e-41
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| DEADc_DDX47 | cd17954 | DEAD-box helicase domain of DEAD box protein 47; DDX47 (also called E4-DEAD box protein) can ... |
61-250 | 2.42e-41 | ||||||
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: 150.54 E-value: 2.42e-41
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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 ... |
61-250 | 4.57e-41 | ||||||
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: 149.68 E-value: 4.57e-41
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| PRK04837 | PRK04837 | ATP-dependent RNA helicase RhlB; Provisional |
61-398 | 4.77e-41 | ||||||
ATP-dependent RNA helicase RhlB; Provisional Pssm-ID: 235314 [Multi-domain] Cd Length: 423 Bit Score: 156.28 E-value: 4.77e-41
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| SF2_C_DEAD | cd18787 | C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse ... |
277-398 | 5.41e-40 | ||||||
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: 143.80 E-value: 5.41e-40
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| PRK04537 | PRK04537 | ATP-dependent RNA helicase RhlB; Provisional |
61-399 | 1.89e-39 | ||||||
ATP-dependent RNA helicase RhlB; Provisional Pssm-ID: 235307 [Multi-domain] Cd Length: 572 Bit Score: 154.72 E-value: 1.89e-39
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| DEADc_DDX19_DDX25 | cd17963 | DEAD-box helicase domain of ATP-dependent RNA helicases DDX19 and DDX25; DDX19 (also called ... |
66-256 | 3.99e-39 | ||||||
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: 143.87 E-value: 3.99e-39
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| DEADc_DDX54 | cd17959 | DEAD-box helicase domain of DEAD box protein 54; DDX54 interacts in a hormone-dependent manner ... |
59-249 | 5.66e-38 | ||||||
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: 140.90 E-value: 5.66e-38
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| DEADc_DDX56 | cd17961 | DEAD-box helicase domain of DEAD box protein 56; DDX56 is a helicase required for assembly of ... |
66-258 | 1.31e-37 | ||||||
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: 139.64 E-value: 1.31e-37
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| DEADc_DDX3_DDX4 | cd17967 | DEAD-box helicase domain of ATP-dependent RNA helicases DDX3 and DDX4; This subfamily includes ... |
66-256 | 1.70e-37 | ||||||
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: 139.93 E-value: 1.70e-37
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| DEADc_DDX52 | cd17957 | DEAD-box helicase domain of DEAD box protein 52; DDX52 (also called ROK1 and HUSSY19) is ... |
70-255 | 1.51e-35 | ||||||
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: 133.48 E-value: 1.51e-35
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| DEADc_DDX24 | cd17946 | DEAD-box helicase domain of DEAD box protein 24; The human DDX24 gene encodes a DEAD box ... |
70-246 | 1.75e-35 | ||||||
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: 134.67 E-value: 1.75e-35
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| PLN00206 | PLN00206 | DEAD-box ATP-dependent RNA helicase; Provisional |
61-404 | 5.89e-35 | ||||||
DEAD-box ATP-dependent RNA helicase; Provisional Pssm-ID: 215103 [Multi-domain] Cd Length: 518 Bit Score: 140.31 E-value: 5.89e-35
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| DEADc_EIF4AIII_DDX48 | cd18045 | DEAD-box helicase domain of eukaryotic initiation factor 4A-III; Eukaryotic initiation factor ... |
61-264 | 2.26e-33 | ||||||
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: 127.58 E-value: 2.26e-33
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| DEADc_DDX42 | cd17952 | DEAD-box helicase domain of DEAD box protein 42; DDX42 (also called Splicing Factor ... |
70-264 | 1.40e-32 | ||||||
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: 125.22 E-value: 1.40e-32
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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, ... |
70-254 | 2.54e-32 | ||||||
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: 124.61 E-value: 2.54e-32
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| DEADc_DDX5_DDX17 | cd17966 | DEAD-box helicase domain of ATP-dependent RNA helicases DDX5 and DDX17; DDX5 and DDX17 are ... |
70-259 | 2.96e-32 | ||||||
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: 124.02 E-value: 2.96e-32
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| DEADc_DDX59 | cd17962 | DEAD-box helicase domain of DEAD box protein 59; DDX59 plays an important role in lung cancer ... |
78-259 | 9.20e-32 | ||||||
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: 122.66 E-value: 9.20e-32
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| DEADc_DDX23 | cd17945 | DEAD-box helicase domain of DEAD box protein 23; DDX23 (also called U5 snRNP 100kD protein and ... |
70-256 | 2.32e-31 | ||||||
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: 122.43 E-value: 2.32e-31
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| PDI_a_family | cd02961 | Protein Disulfide Isomerase (PDIa) family, redox active TRX domains; composed of eukaryotic ... |
552-653 | 1.99e-30 | ||||||
Protein Disulfide Isomerase (PDIa) family, redox active TRX domains; composed of eukaryotic proteins involved in oxidative protein folding in the endoplasmic reticulum (ER) by acting as catalysts and folding assistants. Members of this family include PDI and PDI-related proteins like ERp72, ERp57 (or ERp60), ERp44, P5, PDIR, ERp46 and the transmembrane PDIs. PDI, ERp57, ERp72, P5, PDIR and ERp46 are all oxidases, catalyzing the formation of disulfide bonds of newly synthesized polypeptides in the ER. They also exhibit reductase activity in acting as isomerases to correct any non-native disulfide bonds, as well as chaperone activity to prevent protein aggregation and facilitate the folding of newly synthesized proteins. These proteins usually contain multiple copies of a redox active TRX (a) domain containing a CXXC motif, and may also contain one or more redox inactive TRX-like (b) domains. Only one a domain is required for the oxidase function but multiple copies are necessary for the isomerase function. The different types of PDIs may show different substrate specificities and tissue-specific expression, or may be induced by stress. PDIs are in their reduced form at steady state and are oxidized to the active form by Ero1, which is localized in the ER through ERp44. Some members of this family also contain a DnaJ domain in addition to the redox active a domains; examples are ERdj5 and Pfj2. Also included in the family is the redox inactive N-terminal TRX-like domain of ERp29. Pssm-ID: 239259 [Multi-domain] Cd Length: 101 Bit Score: 115.40 E-value: 1.99e-30
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| DEADc_DDX10 | cd17941 | DEAD-box helicase domain of DEAD box protein 10; Fusion of the DDX10 gene and the nucleoporin ... |
71-254 | 4.84e-30 | ||||||
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: 117.78 E-value: 4.84e-30
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| DEADc_DDX46 | cd17953 | DEAD-box helicase domain of DEAD box protein 46; DDX46 (also called Prp5-like DEAD-box protein) ... |
78-264 | 6.01e-30 | ||||||
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: 118.25 E-value: 6.01e-30
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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 ... |
66-259 | 6.01e-30 | ||||||
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: 119.69 E-value: 6.01e-30
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| ERGIC_N | pfam13850 | Endoplasmic Reticulum-Golgi Intermediate Compartment (ERGIC); This family is the N-terminal of ... |
409-498 | 1.45e-29 | ||||||
Endoplasmic Reticulum-Golgi Intermediate Compartment (ERGIC); This family is the N-terminal of ERGIC proteins, ER-Golgi intermediate compartment clusters, otherwise known as Ervs, and is associated with family COPIIcoated_ERV, pfam07970. Pssm-ID: 464000 Cd Length: 91 Bit Score: 112.55 E-value: 1.45e-29
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| COPIIcoated_ERV | pfam07970 | Endoplasmic reticulum vesicle transporter; This family is conserved from plants and fungi to ... |
684-850 | 1.24e-26 | ||||||
Endoplasmic reticulum vesicle transporter; This family is conserved from plants and fungi to humans. Erv46 works in close conjunction with Erv41 and together they form a complex which cycles between the endoplasmic reticulum and Golgi complex. Erv46-41 interacts strongly with the endoplasmic reticulum glucosidase II. Mammalian glucosidase II comprises a catalytic alpha-subunit and a 58 kDa beta subunit, which is required for ER localization. All proteins identified biochemically as Erv41p-Erv46p interactors are localized to the early secretory pathway and are involved in protein maturation and processing in the ER and/or sorting into COPII vesicles for transport to the Golgi. Pssm-ID: 462327 Cd Length: 225 Bit Score: 108.85 E-value: 1.24e-26
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| Helicase_C | pfam00271 | Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ... |
303-398 | 1.80e-26 | ||||||
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: 104.21 E-value: 1.80e-26
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| DEADc_DDX41 | cd17951 | DEAD-box helicase domain of DEAD box protein 41; DDX41 (also called ABS and MPLPF) interacts ... |
70-245 | 5.13e-26 | ||||||
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: 106.65 E-value: 5.13e-26
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| DEADc_DDX3 | cd18051 | DEAD-box helicase domain of DEAD box protein 3; DDX3 (also called helicase-like protein, DEAD ... |
57-259 | 1.50e-25 | ||||||
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: 106.28 E-value: 1.50e-25
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| DEADc_DDX5 | cd18049 | DEAD-box helicase domain of DEAD box protein 5; DDX5 (also called RNA helicase P68, HLR1, ... |
70-259 | 2.89e-25 | ||||||
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: 105.09 E-value: 2.89e-25
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| ER_PDI_fam | TIGR01130 | protein disulfide isomerase, eukaryotic; This model represents eukaryotic protein disulfide ... |
549-657 | 3.26e-25 | ||||||
protein disulfide isomerase, eukaryotic; This model represents eukaryotic protein disulfide isomerases retained in the endoplasmic reticulum (ER) and closely related forms. Some members have been assigned alternative or additional functions such as prolyl 4-hydroxylase and dolichyl-diphosphooligosaccharide-protein glycotransferase. Members of this family have at least two protein-disulfide domains, each similar to thioredoxin but with the redox-active disulfide in the motif PWCGHCK, and an ER retention signal at the extreme C-terminus (KDEL, HDEL, and similar motifs). Pssm-ID: 273457 [Multi-domain] Cd Length: 462 Bit Score: 110.15 E-value: 3.26e-25
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| DEADc_DDX43_DDX53 | cd17958 | DEAD-box helicase domain of DEAD box proteins 43 and 53; DDX43 (also called cancer/testis ... |
70-265 | 6.87e-25 | ||||||
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: 102.93 E-value: 6.87e-25
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| PDI_a_ERp46 | cd03005 | PDIa family, endoplasmic reticulum protein 46 (ERp46) subfamily; ERp46 is an ER-resident ... |
549-653 | 1.28e-24 | ||||||
PDIa family, endoplasmic reticulum protein 46 (ERp46) subfamily; ERp46 is an ER-resident protein containing three redox active TRX domains. Yeast complementation studies show that ERp46 can substitute for protein disulfide isomerase (PDI) function in vivo. It has been detected in many tissues, however, transcript and protein levels do not correlate in all tissues, suggesting regulation at a posttranscriptional level. An identical protein, named endoPDI, has been identified as an endothelial PDI that is highly expressed in the endothelium of tumors and hypoxic lesions. It has a protective effect on cells exposed to hypoxia. Pssm-ID: 239303 [Multi-domain] Cd Length: 102 Bit Score: 98.90 E-value: 1.28e-24
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| DEADc_DDX19 | cd18047 | DEAD-box helicase domain of DEAD box protein 19; DDX19 is an RNA helicase involved in both ... |
61-249 | 3.56e-24 | ||||||
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: 101.34 E-value: 3.56e-24
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| DEADc_DDX17 | cd18050 | DEAD-box helicase domain of DEAD box protein 17; DDX17 (also called DEAD Box Protein P72 or ... |
55-256 | 1.32e-23 | ||||||
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: 101.63 E-value: 1.32e-23
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| HELICc | smart00490 | helicase superfamily c-terminal domain; |
317-398 | 1.39e-23 | ||||||
helicase superfamily c-terminal domain; Pssm-ID: 197757 [Multi-domain] Cd Length: 82 Bit Score: 94.97 E-value: 1.39e-23
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| DEADc_DDX18 | cd17942 | DEAD-box helicase domain of DEAD box protein 18; This DDX18 gene encodes a DEAD box protein ... |
71-267 | 4.74e-23 | ||||||
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: 97.82 E-value: 4.74e-23
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| PDI_a_ERp38 | cd02998 | PDIa family, endoplasmic reticulum protein 38 (ERp38) subfamily; composed of proteins similar ... |
552-653 | 5.28e-23 | ||||||
PDIa family, endoplasmic reticulum protein 38 (ERp38) subfamily; composed of proteins similar to the P5-like protein first isolated from alfalfa, which contains two redox active TRX (a) domains at the N-terminus, like human P5, and a C-terminal domain with homology to the C-terminal domain of ERp29, unlike human P5. The cDNA clone of this protein (named G1) was isolated from an alfalfa cDNA library by screening with human protein disulfide isomerase (PDI) cDNA. The G1 protein is constitutively expressed in all major organs of the plant and its expression is induced by treatment with tunicamycin, indicating that it may be a glucose-regulated protein. The G1 homolog in the eukaryotic social amoeba Dictyostelium discoideum is also described as a P5-like protein, which is located in the endoplasmic reticulum (ER) despite the absence of an ER-retrieval signal. G1 homologs from Aspergillus niger and Neurospora crassa have also been characterized, and are named TIGA and ERp38, respectively. Also included in the alignment is an atypical PDI from Leishmania donovani containing a single a domain, and the C-terminal a domain of a P5-like protein from Entamoeba histolytica. Pssm-ID: 239296 [Multi-domain] Cd Length: 105 Bit Score: 94.24 E-value: 5.28e-23
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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 ... |
96-256 | 7.84e-23 | ||||||
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: 97.23 E-value: 7.84e-23
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| DEADc_DDX25 | cd18048 | DEAD-box helicase domain of DEAD box protein 25; DDX25 (also called gonadotropin-regulated ... |
61-249 | 1.04e-22 | ||||||
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: 97.78 E-value: 1.04e-22
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| DEADc_DDX31 | cd17949 | DEAD-box helicase domain of DEAD box protein 31; DDX31 (also called helicain or G2 helicase) ... |
78-249 | 6.58e-22 | ||||||
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: 94.96 E-value: 6.58e-22
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| PDI_a_PDIR | cd02997 | PDIa family, PDIR subfamily; composed of proteins similar to human PDIR (for Protein Disulfide ... |
548-653 | 1.51e-20 | ||||||
PDIa family, PDIR subfamily; composed of proteins similar to human PDIR (for Protein Disulfide Isomerase Related). PDIR is composed of three redox active TRX (a) domains and an N-terminal redox inactive TRX-like (b) domain. Similar to PDI, it is involved in oxidative protein folding in the endoplasmic reticulum (ER) through its isomerase and chaperone activities. These activities are lower compared to PDI, probably due to PDIR acting only on a subset of proteins. PDIR is preferentially expressed in cells actively secreting proteins and its expression is induced by stress. Similar to PDI, the isomerase and chaperone activities of PDIR are independent; CXXC mutants lacking isomerase activity retain chaperone activity. Pssm-ID: 239295 [Multi-domain] Cd Length: 104 Bit Score: 87.37 E-value: 1.51e-20
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| PTZ00102 | PTZ00102 | disulphide isomerase; Provisional |
549-653 | 1.37e-19 | ||||||
disulphide isomerase; Provisional Pssm-ID: 240266 [Multi-domain] Cd Length: 477 Bit Score: 92.89 E-value: 1.37e-19
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| PDI_a_P5 | cd03001 | PDIa family, P5 subfamily; composed of eukaryotic proteins similar to human P5, a PDI-related ... |
553-648 | 7.48e-19 | ||||||
PDIa family, P5 subfamily; composed of eukaryotic proteins similar to human P5, a PDI-related protein with a domain structure of aa'b (where a and a' are redox active TRX domains and b is a redox inactive TRX-like domain). Like PDI, P5 is located in the endoplasmic reticulum (ER) and displays both isomerase and chaperone activities, which are independent of each other. Compared to PDI, the isomerase and chaperone activities of P5 are lower. The first cysteine in the CXXC motif of both redox active domains in P5 is necessary for isomerase activity. The P5 gene was first isolated as an amplified gene from a hydroxyurea-resistant hamster cell line. The zebrafish P5 homolog has been implicated to play a critical role in establishing left/right asymmetries in the embryonic midline. Some members of this subfamily are P5-like proteins containing only one redox active TRX domain. Pssm-ID: 239299 [Multi-domain] Cd Length: 103 Bit Score: 82.33 E-value: 7.48e-19
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| DEADc_DDX28 | cd17948 | DEAD-box helicase domain of DEAD box protein 28; DDX28 (also called mitochondrial DEAD-box ... |
78-245 | 3.62e-17 | ||||||
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: 81.64 E-value: 3.62e-17
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| PDI_a_MPD1_like | cd03002 | PDI family, MPD1-like subfamily; composed of eukaryotic proteins similar to Saccharomyces ... |
553-654 | 6.61e-17 | ||||||
PDI family, MPD1-like subfamily; composed of eukaryotic proteins similar to Saccharomyces cerevisiae MPD1 protein, which contains a single redox active TRX domain located at the N-terminus, and an ER retention signal at the C-terminus indicative of an ER-resident protein. MPD1 has been shown to suppress the maturation defect of carboxypeptidase Y caused by deletion of the yeast PDI1 gene. Other characterized members of this subfamily include the Aspergillus niger prpA protein and Giardia PDI-1. PrpA is non-essential to strain viability, however, its transcript level is induced by heterologous protein expression suggesting a possible role in oxidative protein folding during high protein production. Giardia PDI-1 has the ability to refold scrambled RNase and exhibits transglutaminase activity. Pssm-ID: 239300 [Multi-domain] Cd Length: 109 Bit Score: 77.02 E-value: 6.61e-17
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| Thioredoxin | pfam00085 | Thioredoxin; Thioredoxins are small enzymes that participate in redox reactions, via the ... |
551-653 | 3.99e-16 | ||||||
Thioredoxin; Thioredoxins are small enzymes that participate in redox reactions, via the reversible oxidation of an active centre disulfide bond. Some members with only the active site are not separated from the noise. Pssm-ID: 395038 [Multi-domain] Cd Length: 103 Bit Score: 74.58 E-value: 3.99e-16
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| PDI_a_ERp44 | cd02996 | PDIa family, endoplasmic reticulum protein 44 (ERp44) subfamily; ERp44 is an ER-resident ... |
553-653 | 4.11e-16 | ||||||
PDIa family, endoplasmic reticulum protein 44 (ERp44) subfamily; ERp44 is an ER-resident protein, induced during stress, involved in thiol-mediated ER retention. It contains an N-terminal TRX domain, similar to that of PDIa, with a CXFS motif followed by two redox inactive TRX-like domains, homologous to the b and b' domains of PDI. The CXFS motif in the N-terminal domain allows ERp44 to form stable reversible mixed disulfides with its substrates. Through this activity, ERp44 mediates the ER localization of Ero1alpha, a protein that oxidizes protein disulfide isomerases into their active form. ERp44 also prevents the secretion of unassembled cargo protein with unpaired cysteines. It also modulates the activity of inositol 1,4,5-triphosphate type I receptor (IP3R1), an intracellular channel protein that mediates calcium release from the ER to the cytosol. Pssm-ID: 239294 [Multi-domain] Cd Length: 108 Bit Score: 74.73 E-value: 4.11e-16
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| PDI_a_ERdj5_C | cd03004 | PDIa family, C-terminal ERdj5 subfamily; ERdj5, also known as JPDI and macrothioredoxin, is a ... |
549-643 | 6.54e-16 | ||||||
PDIa family, C-terminal ERdj5 subfamily; ERdj5, also known as JPDI and macrothioredoxin, is a protein containing an N-terminal DnaJ domain and four redox active TRX domains. This subfamily is composed of the three TRX domains located at the C-terminal half of the protein. ERdj5 is a ubiquitous protein localized in the endoplasmic reticulum (ER) and is abundant in secretory cells. It's transcription is induced during ER stress. It interacts with BiP through its DnaJ domain in an ATP-dependent manner. BiP, an ER-resident member of the Hsp70 chaperone family, functions in ER-associated degradation and protein translocation. Also included in the alignment is the single complete TRX domain of an uncharacterized protein from Tetraodon nigroviridis, which also contains a DnaJ domain at its N-terminus. Pssm-ID: 239302 [Multi-domain] Cd Length: 104 Bit Score: 74.25 E-value: 6.54e-16
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| ER_PDI_fam | TIGR01130 | protein disulfide isomerase, eukaryotic; This model represents eukaryotic protein disulfide ... |
552-653 | 7.48e-16 | ||||||
protein disulfide isomerase, eukaryotic; This model represents eukaryotic protein disulfide isomerases retained in the endoplasmic reticulum (ER) and closely related forms. Some members have been assigned alternative or additional functions such as prolyl 4-hydroxylase and dolichyl-diphosphooligosaccharide-protein glycotransferase. Members of this family have at least two protein-disulfide domains, each similar to thioredoxin but with the redox-active disulfide in the motif PWCGHCK, and an ER retention signal at the extreme C-terminus (KDEL, HDEL, and similar motifs). Pssm-ID: 273457 [Multi-domain] Cd Length: 462 Bit Score: 81.26 E-value: 7.48e-16
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| PDI_a_PDI_a'_C | cd02995 | PDIa family, C-terminal TRX domain (a') subfamily; composed of the C-terminal redox active a' ... |
552-653 | 8.14e-16 | ||||||
PDIa family, C-terminal TRX domain (a') subfamily; composed of the C-terminal redox active a' domains of PDI, ERp72, ERp57 (or ERp60) and EFP1. PDI, ERp72 and ERp57 are endoplasmic reticulum (ER)-resident eukaryotic proteins involved in oxidative protein folding. They are oxidases, catalyzing the formation of disulfide bonds of newly synthesized polypeptides in the ER. They also exhibit reductase activity in acting as isomerases to correct any non-native disulfide bonds, as well as chaperone activity to prevent protein aggregation and facilitate the folding of newly synthesized proteins. PDI and ERp57 have the abb'a' domain structure (where a and a' are redox active TRX domains while b and b' are redox inactive TRX-like domains). PDI also contains an acidic region (c domain) after the a' domain that is absent in ERp57. ERp72 has an additional a domain at the N-terminus (a"abb'a' domain structure). ERp57 interacts with the lectin chaperones, calnexin and calreticulin, and specifically promotes the oxidative folding of glycoproteins, while PDI shows a wider substrate specificity. ERp72 associates with several ER chaperones and folding factors to form complexes in the ER that bind nascent proteins. EFP1 is a binding partner protein of thyroid oxidase, which is responsible for the generation of hydrogen peroxide, a crucial substrate of thyroperoxidase, which functions to iodinate thyroglobulin and synthesize thyroid hormones. Pssm-ID: 239293 [Multi-domain] Cd Length: 104 Bit Score: 73.74 E-value: 8.14e-16
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| DEADc_DDX51 | cd17956 | DEAD-box helicase domain of DEAD box protein 51; DDX51 aids cell cancer proliferation by ... |
70-246 | 1.06e-15 | ||||||
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: 77.29 E-value: 1.06e-15
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| PTZ00443 | PTZ00443 | Thioredoxin domain-containing protein; Provisional |
545-662 | 1.20e-15 | ||||||
Thioredoxin domain-containing protein; Provisional Pssm-ID: 185622 [Multi-domain] Cd Length: 224 Bit Score: 76.97 E-value: 1.20e-15
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| CnoX | COG3118 | Chaperedoxin CnoX, contains thioredoxin-like and TPR-like domains, YbbN/TrxSC family ... |
553-630 | 1.81e-15 | ||||||
Chaperedoxin CnoX, contains thioredoxin-like and TPR-like domains, YbbN/TrxSC family [Posttranslational modification, protein turnover, chaperones]; Pssm-ID: 442352 [Multi-domain] Cd Length: 105 Bit Score: 72.93 E-value: 1.81e-15
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| SF2-N | cd00046 | N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ... |
102-244 | 2.32e-15 | ||||||
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: 73.98 E-value: 2.32e-15
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| SSL2 | COG1061 | Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair]; |
100-375 | 1.24e-13 | ||||||
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair]; Pssm-ID: 440681 [Multi-domain] Cd Length: 566 Bit Score: 74.68 E-value: 1.24e-13
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| PDI_a_TMX3 | cd03000 | PDIa family, TMX3 subfamily; composed of eukaryotic proteins similar to human TMX3, a TRX ... |
566-652 | 2.29e-13 | ||||||
PDIa family, TMX3 subfamily; composed of eukaryotic proteins similar to human TMX3, a TRX related transmembrane protein containing one redox active TRX domain at the N-terminus and a classical ER retrieval sequence for type I transmembrane proteins at the C-terminus. The TMX3 transcript is found in a variety of tissues with the highest levels detected in skeletal muscle and the heart. In vitro, TMX3 showed oxidase activity albeit slightly lower than that of protein disulfide isomerase. Pssm-ID: 239298 [Multi-domain] Cd Length: 104 Bit Score: 66.71 E-value: 2.29e-13
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| PDI_a_TMX | cd02994 | PDIa family, TMX subfamily; composed of proteins similar to the TRX-related human ... |
552-653 | 5.01e-12 | ||||||
PDIa family, TMX subfamily; composed of proteins similar to the TRX-related human transmembrane protein, TMX. TMX is a type I integral membrane protein; the N-terminal redox active TRX domain is present in the endoplasmic reticulum (ER) lumen while the C-terminus is oriented towards the cytoplasm. It is expressed in many cell types and its active site motif (CPAC) is unique. In vitro, TMX reduces interchain disulfides of insulin and renatures inactive RNase containing incorrect disulfide bonds. The C. elegans homolog, DPY-11, is expressed only in the hypodermis and resides in the cytoplasm. It is required for body and sensory organ morphogeneis. Another uncharacterized TRX-related transmembrane protein, human TMX4, is included in the alignment. The active site sequence of TMX4 is CPSC. Pssm-ID: 239292 [Multi-domain] Cd Length: 101 Bit Score: 62.78 E-value: 5.01e-12
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| PDI_a_QSOX | cd02992 | PDIa family, Quiescin-sulfhydryl oxidase (QSOX) subfamily; QSOX is a eukaryotic protein ... |
552-653 | 7.56e-12 | ||||||
PDIa family, Quiescin-sulfhydryl oxidase (QSOX) subfamily; QSOX is a eukaryotic protein containing an N-terminal redox active TRX domain, similar to that of PDI, and a small C-terminal flavin adenine dinucleotide (FAD)-binding domain homologous to the yeast ERV1p protein. QSOX oxidizes thiol groups to disulfides like PDI, however, unlike PDI, this oxidation is accompanied by the reduction of oxygen to hydrogen peroxide. QSOX is localized in high concentrations in cells with heavy secretory load and prefers peptides and proteins as substrates, not monothiols like glutathione. Inside the cell, QSOX is found in the endoplasmic reticulum and Golgi. The flow of reducing equivalents in a QSOX-catalyzed reaction goes from the dithiol substrate -> dithiol of the QSOX TRX domain -> dithiols of the QSOX ERV1p domain -> FAD -> oxygen. Pssm-ID: 239290 [Multi-domain] Cd Length: 114 Bit Score: 62.67 E-value: 7.56e-12
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| TRX_family | cd02947 | TRX family; composed of two groups: Group I, which includes proteins that exclusively encode a ... |
556-637 | 1.47e-10 | ||||||
TRX family; composed of two groups: Group I, which includes proteins that exclusively encode a TRX domain; and Group II, which are composed of fusion proteins of TRX and additional domains. Group I TRX is a small ancient protein that alter the redox state of target proteins via the reversible oxidation of an active site dithiol, present in a CXXC motif, partially exposed at the protein's surface. TRX reduces protein disulfide bonds, resulting in a disulfide bond at its active site. Oxidized TRX is converted to the active form by TRX reductase, using reducing equivalents derived from either NADPH or ferredoxins. By altering their redox state, TRX regulates the functions of at least 30 target proteins, some of which are enzymes and transcription factors. It also plays an important role in the defense against oxidative stress by directly reducing hydrogen peroxide and certain radicals, and by serving as a reductant for peroxiredoxins. At least two major types of functional TRXs have been reported in most organisms; in eukaryotes, they are located in the cytoplasm and the mitochondria. Higher plants contain more types (at least 20 TRX genes have been detected in the genome of Arabidopsis thaliana), two of which (types f amd m) are located in the same compartment, the chloroplast. Also included in the alignment are TRX-like domains which show sequence homology to TRX but do not contain the redox active CXXC motif. Group II proteins, in addition to either a redox active TRX or a TRX-like domain, also contain additional domains, which may or may not possess homology to known proteins. Pssm-ID: 239245 [Multi-domain] Cd Length: 93 Bit Score: 58.34 E-value: 1.47e-10
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| SF2_C_EcoAI-like | cd18799 | C-terminal helicase domain of EcoAI HsdR-like restriction enzyme family helicases; This family ... |
307-375 | 5.34e-08 | ||||||
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: 51.79 E-value: 5.34e-08
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| TRX_superfamily | cd01659 | Thioredoxin (TRX) superfamily; a large, diverse group of proteins containing a TRX-fold. Many ... |
569-631 | 2.02e-07 | ||||||
Thioredoxin (TRX) superfamily; a large, diverse group of proteins containing a TRX-fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include TRX, protein disulfide isomerase (PDI), tlpA-like, glutaredoxin, NrdH redoxin, and the bacterial Dsb (DsbA, DsbC, DsbG, DsbE, DsbDgamma) protein families. Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins and glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others. Pssm-ID: 238829 [Multi-domain] Cd Length: 69 Bit Score: 48.85 E-value: 2.02e-07
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| PTZ00102 | PTZ00102 | disulphide isomerase; Provisional |
573-666 | 2.06e-07 | ||||||
disulphide isomerase; Provisional Pssm-ID: 240266 [Multi-domain] Cd Length: 477 Bit Score: 54.37 E-value: 2.06e-07
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| PDI_a_ERdj5_N | cd03003 | PDIa family, N-terminal ERdj5 subfamily; ERdj5, also known as JPDI and macrothioredoxin, is a ... |
553-647 | 3.18e-07 | ||||||
PDIa family, N-terminal ERdj5 subfamily; ERdj5, also known as JPDI and macrothioredoxin, is a protein containing an N-terminal DnaJ domain and four redox active TRX domains. This subfamily is comprised of the first TRX domain of ERdj5 located after the DnaJ domain at the N-terminal half of the protein. ERdj5 is a ubiquitous protein localized in the endoplasmic reticulum (ER) and is abundant in secretory cells. It's transcription is induced during ER stress. It interacts with BiP through its DnaJ domain in an ATP-dependent manner. BiP, an ER-resident member of the Hsp70 chaperone family, functions in ER-associated degradation and protein translocation. Pssm-ID: 239301 [Multi-domain] Cd Length: 101 Bit Score: 49.45 E-value: 3.18e-07
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| RecQ | COG0514 | Superfamily II DNA helicase RecQ [Replication, recombination and repair]; |
306-398 | 4.52e-07 | ||||||
Superfamily II DNA helicase RecQ [Replication, recombination and repair]; Pssm-ID: 440280 [Multi-domain] Cd Length: 489 Bit Score: 53.22 E-value: 4.52e-07
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| ybbN | cd02956 | ybbN protein family; ybbN is a hypothetical protein containing a redox-inactive TRX-like ... |
556-653 | 1.67e-06 | ||||||
ybbN protein family; ybbN is a hypothetical protein containing a redox-inactive TRX-like domain. Its gene has been sequenced from several gammaproteobacteria and actinobacteria. Pssm-ID: 239254 [Multi-domain] Cd Length: 96 Bit Score: 46.88 E-value: 1.67e-06
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| SF2_C | cd18785 | C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases ... |
355-398 | 1.76e-06 | ||||||
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: 46.54 E-value: 1.76e-06
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| Cas3_I | cd09639 | CRISPR/Cas system-associated protein Cas3; CRISPR (Clustered Regularly Interspaced Short ... |
238-368 | 5.04e-06 | ||||||
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: 49.74 E-value: 5.04e-06
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| PTZ00051 | PTZ00051 | thioredoxin; Provisional |
552-630 | 5.76e-06 | ||||||
thioredoxin; Provisional Pssm-ID: 173347 [Multi-domain] Cd Length: 98 Bit Score: 45.64 E-value: 5.76e-06
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| PDI_a_APS_reductase | cd02993 | PDIa family, 5'-Adenylylsulfate (APS) reductase subfamily; composed of plant-type APS ... |
568-653 | 1.10e-05 | ||||||
PDIa family, 5'-Adenylylsulfate (APS) reductase subfamily; composed of plant-type APS reductases containing a C-terminal redox active TRX domain and an N-terminal reductase domain which is part of a superfamily that includes N type ATP PPases. APS reductase catalyzes the reduction of activated sulfate to sulfite, a key step in the biosynthesis of sulfur-containing metabolites. Sulfate is first activated by ATP sulfurylase, forming APS, which can be phosphorylated to 3'-phosphoadenosine-5'-phosphosulfate (PAPS). Depending on the organism, either APS or PAPS can be used for sulfate reduction. Prokaryotes and fungi use PAPS, whereas plants use both APS and PAPS. Since plant-type APS reductase uses glutathione (GSH) as its electron donor, the C-terminal domain may function like glutaredoxin, a GSH-dependent member of the TRX superfamily. The flow of reducing equivalents goes from GSH -> C-terminal TRX domain -> N-terminal reductase domain -> APS. Plant-type APS reductase shows no homology to that of dissimilatory sulfate-reducing bacteria, which is an iron-sulfur flavoenzyme. Also included in the alignment is EYE2 from Chlamydomonas reinhardtii, a protein required for eyespot assembly. Pssm-ID: 239291 [Multi-domain] Cd Length: 109 Bit Score: 45.14 E-value: 1.10e-05
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| PDI_a_ERp44_like | cd02999 | PDIa family, endoplasmic reticulum protein 44 (ERp44)-like subfamily; composed of ... |
563-647 | 1.96e-05 | ||||||
PDIa family, endoplasmic reticulum protein 44 (ERp44)-like subfamily; composed of uncharacterized PDI-like eukaryotic proteins containing only one redox active TRX (a) domain with a CXXS motif, similar to ERp44. CXXS is still a redox active motif; however, the mixed disulfide formed with the substrate is more stable than those formed by CXXC motif proteins. PDI-related proteins are usually involved in the oxidative protein folding in the ER by acting as catalysts and folding assistants. ERp44 is involved in thiol-mediated retention in the ER. Pssm-ID: 239297 [Multi-domain] Cd Length: 100 Bit Score: 44.27 E-value: 1.96e-05
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| PLN02309 | PLN02309 | 5'-adenylylsulfate reductase |
503-630 | 3.86e-05 | ||||||
5'-adenylylsulfate reductase Pssm-ID: 215175 [Multi-domain] Cd Length: 457 Bit Score: 47.09 E-value: 3.86e-05
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| cas3_core | TIGR01587 | CRISPR-associated helicase Cas3; This model represents the highly conserved core region of an ... |
238-398 | 5.10e-05 | ||||||
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: 46.29 E-value: 5.10e-05
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| SF2_C_RecQ | cd18794 | C-terminal helicase domain of the RecQ family helicases; The RecQ helicase family is an ... |
306-398 | 5.14e-05 | ||||||
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: 43.74 E-value: 5.14e-05
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| DEXHc_dicer | cd18034 | DEXH-box helicase domain of endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded ... |
99-212 | 6.33e-04 | ||||||
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: 41.87 E-value: 6.33e-04
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| MPH1 | COG1111 | ERCC4-related helicase [Replication, recombination and repair]; |
106-212 | 7.91e-04 | ||||||
ERCC4-related helicase [Replication, recombination and repair]; Pssm-ID: 440728 [Multi-domain] Cd Length: 718 Bit Score: 43.18 E-value: 7.91e-04
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| Thioredoxin_2 | pfam13098 | Thioredoxin-like domain; |
564-633 | 1.02e-03 | ||||||
Thioredoxin-like domain; Pssm-ID: 379034 [Multi-domain] Cd Length: 103 Bit Score: 39.33 E-value: 1.02e-03
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| CMS1 | pfam14617 | U3-containing 90S pre-ribosomal complex subunit; This is a family of fungal and plant ... |
116-229 | 1.60e-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: 1.60e-03
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| SF2_C_FANCM_Hef | cd18801 | C-terminal helicase domain of Fanconi anemia group M family helicases; Fanconi anemia group M ... |
305-398 | 2.25e-03 | ||||||
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: 39.26 E-value: 2.25e-03
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| PRK09751 | PRK09751 | putative ATP-dependent helicase Lhr; Provisional |
333-427 | 3.03e-03 | ||||||
putative ATP-dependent helicase Lhr; Provisional Pssm-ID: 137505 [Multi-domain] Cd Length: 1490 Bit Score: 41.45 E-value: 3.03e-03
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| TrxA | COG0526 | Thiol-disulfide isomerase or thioredoxin [Posttranslational modification, protein turnover, ... |
568-592 | 4.70e-03 | ||||||
Thiol-disulfide isomerase or thioredoxin [Posttranslational modification, protein turnover, chaperones]; Pssm-ID: 440292 [Multi-domain] Cd Length: 139 Bit Score: 38.13 E-value: 4.70e-03
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| PRK11057 | PRK11057 | ATP-dependent DNA helicase RecQ; Provisional |
333-412 | 5.06e-03 | ||||||
ATP-dependent DNA helicase RecQ; Provisional Pssm-ID: 182933 [Multi-domain] Cd Length: 607 Bit Score: 40.47 E-value: 5.06e-03
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| PRK13766 | PRK13766 | Hef nuclease; Provisional |
106-212 | 6.60e-03 | ||||||
Hef nuclease; Provisional Pssm-ID: 237496 [Multi-domain] Cd Length: 773 Bit Score: 40.24 E-value: 6.60e-03
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| DEXHc_RE | cd17926 | DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family ... |
106-212 | 6.69e-03 | ||||||
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: 38.06 E-value: 6.69e-03
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| MPH1 | COG1111 | ERCC4-related helicase [Replication, recombination and repair]; |
336-378 | 6.79e-03 | ||||||
ERCC4-related helicase [Replication, recombination and repair]; Pssm-ID: 440728 [Multi-domain] Cd Length: 718 Bit Score: 40.10 E-value: 6.79e-03
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| SF2_C_RecG | cd18811 | C-terminal helicase domain of DNA helicase RecG; ATP-dependent DNA helicase RecG plays a ... |
332-398 | 6.86e-03 | ||||||
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: 38.09 E-value: 6.86e-03
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| SoxW | COG2143 | Thioredoxin-related protein SoxW [Posttranslational modification, protein turnover, chaperones] ... |
569-653 | 7.70e-03 | ||||||
Thioredoxin-related protein SoxW [Posttranslational modification, protein turnover, chaperones]; Pssm-ID: 441746 [Multi-domain] Cd Length: 146 Bit Score: 37.96 E-value: 7.70e-03
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