SII-SWORD/CoKE huggingface dataset:
EIF2AK2, first double-stranded RNA binding domain (EIF2AK2_DSRM_1)
Type: Domain

Eukaryotic translation initiation factor 2-alpha kinase 2 (EIF2AK2), also known as PKR, is an IFN-induced dsRNA-dependent serine/threonine-protein kinase that phosphorylates the alpha subunit of eukaryotic translation initiation factor 2 (EIF2S1/eIF-2-alpha) and plays a key role in the innate immune response to viral infection . It is also involved in the regulation of signal transduction, apoptosis, cell proliferation and differentiation . EIF2AK2 proteins contain two to three double-stranded RNA binding motifs (DSRMs).

This entry represents the first DSRM of EIF2AK2.
EIF2AK2, second double-stranded RNA binding domain (EIF2AK2_DSRM_2)
Type: Domain

Eukaryotic translation initiation factor 2-alpha kinase 2 (EIF2AK2), also known as PKR, is an IFN-induced dsRNA-dependent serine/threonine-protein kinase that phosphorylates the alpha subunit of eukaryotic translation initiation factor 2 (EIF2S1/eIF-2-alpha) and plays a key role in the innate immune response to viral infection . It is also involved in the regulation of signal transduction, apoptosis, cell proliferation and differentiation . EIF2AK2 proteins contain two to three double-stranded RNA binding motifs (DSRMs).

This entry represents the second DSRM of EIF2AK2.
ADAD2, double-stranded RNA binding domain (ADAD2_DSRM)
Type: Domain

Adenosine deaminase domain containing 2 (ADAD2) is phylogenetically related to a family of adenosine deaminases involved in RNA editing. It is a double-stranded RNA binding protein with unclear biological function . ADAD2 contains a double-stranded RNA binding motif (DSRM) and a C-terminal adenosine-deaminase (editase) domain. This entry represents the DSRM of ADAD2.
ADAD1, double-stranded RNA binding domain (ADAD1_DSRM)
Type: Domain

Adenosine deaminase domain containing 1 (ADAD1), also known as testis nuclear RNA-binding protein (TENR), is phylogenetically related to a family of adenosine deaminases involved in RNA editing. It plays an essential function in spermatid morphogenesis. It may be involved in testis-specific nuclear post-transcriptional processes such as heterogeneous nuclear RNA (hnRNA) packaging, alternative splicing, or nuclear/cytoplasmic transport of mRNAs . ADAD1 contains a double-stranded RNA binding motif (DSRM) and a C-terminal adenosine-deaminase (editase) domain. This entry represents the DSRM of ADAD1.
ADAR1, first double-stranded RNA binding domain (ADAR1_DSRM_1)
Type: Domain

Adenosine-to-inosine (A-to-I) editing is a post-transcriptional modification of RNA which changes its sequence, coding potential and secondary structure. A-to-I editing occurs at approximately 50 000-150 000 sites in mice and into the millions of sites in humans. This reaction is catalysed by the adenosine deaminase acting on RNA (ADAR) proteins, ADAR1 and ADAR2 . ADAR1 and ADAR2 can edit both viral and cellular RNAs and can edit RNAs at multiple sites (hyper-editing) or at specific sites (site-specific editing) .

ADAR1 contains three double-stranded RNA binding motifs (DSRMs). This entry represents the first DSRM of ADAR1 (also known as DRADA).
ADAR1, third double-stranded RNA binding domain (ADAR1_DSRM_3)
Type: Domain

Adenosine-to-inosine (A-to-I) editing is a post-transcriptional modification of RNA which changes its sequence, coding potential and secondary structure. A-to-I editing occurs at approximately 50 000-150 000 sites in mice and into the millions of sites in humans. This reaction is catalysed by the adenosine deaminase acting on RNA (ADAR) proteins, ADAR1 and ADAR2 . ADAR1 and ADAR2 can edit both viral and cellular RNAs and can edit RNAs at multiple sites (hyper-editing) or at specific sites (site-specific editing) .

ADAR1 contains three double-stranded RNA binding motifs (DSRMs). This entry represents the third DSRM of ADAR1 (also known as DRADA).
ADAR2, first double-stranded RNA binding domain (ADAR2_DSRM_1)
Type: Domain

Adenosine-to-inosine (A-to-I) editing is a post-transcriptional modification of RNA which changes its sequence, coding potential and secondary structure. A-to-I editing occurs at approximately 50 000-150 000 sites in mice and into the millions of sites in humans. This reaction is catalysed by the adenosine deaminase acting on RNA (ADAR) proteins, ADAR1 and ADAR2 . ADAR1 and ADAR2 can edit both viral and cellular RNAs and can edit RNAs at multiple sites (hyper-editing) or at specific sites (site-specific editing) .

ADAR2 contains two double-stranded RNA binding motifs (DSRMs). This entry represents the first DSRM of ADAR2 (also known as RED1).
ADAR2, second double-stranded RNA binding domain (ADAR2_DSRM_2)
Type: Domain

Adenosine-to-inosine (A-to-I) editing is a post-transcriptional modification of RNA which changes its sequence, coding potential and secondary structure. A-to-I editing occurs at approximately 50 000-150 000 sites in mice and into the millions of sites in humans. This reaction is catalysed by the adenosine deaminase acting on RNA (ADAR) proteins, ADAR1 and ADAR2 . ADAR1 and ADAR2 can edit both viral and cellular RNAs and can edit RNAs at multiple sites (hyper-editing) or at specific sites (site-specific editing) .

ADAR2 contains two double-stranded RNA binding motifs (DSRMs). This entry represents the second DSRM of ADAR2 (also known as RED1).
ADAR3, first double-stranded RNA binding domain (ADAR3_DSRM_1)
Type: Domain

Adenosine-to-inosine (A-to-I) editing is a post-transcriptional modification of RNA which changes its sequence, coding potential and secondary structure. This reaction is catalysed by the adenosine deaminase acting on RNA (ADAR) proteins, ADAR1 and ADAR2 . ADAR3 (also known as RED2 or ADARB2) prevents the binding of other ADAR enzymes to targets in vitro, and decreases the efficiency of these enzymes. It is capable of binding to both dsRNA and ssRNA. Moreover, ADAR3 lacks editing activity for currently known substrate RNAs, and may have an inactive editase domain. .

ADAR3 contains two double-stranded RNA binding motifs (DSRMs) and a C-terminal RNA-specific adenosine-deaminase (editase) domain. This entry describes the first DSRM.
A1CF, double-stranded RNA binding domain (A1CF_DSRM)
Type: Domain

APOBEC1 complementation factor (A1CF or ACF) and APOBEC1 (an RNA-binding cytidine deaminase) form the apolipoprotein B (apoB) mRNA editing enzyme complex, which is responsible for the postranscriptional editing of a CAA codon for Gln to a UAA codon for stop in apoB mRNA . APOBEC1 alone induces nonsense-mediated decay (NMD), while the APOBEC1-ACF complex edits and remains associated with the edited RNA to protect it from NMD . ACF has been shown to bind with high affinity to single-stranded but not double-stranded apoB mRNA .

A1CF contains three RNA recognition motifs (RRMs) and a C-terminal double-stranded RNA binding motif (DSRM). This entry represents the DSRM of A1CF.
RBM46, double-stranded RNA binding domain (RBM46_DSR)
Type: Domain

This entry represents the C-terminal double-stranded RNA binding motif (DSR) of RBM46.

RNA-binding motif protein 46 (RBM46), also known as cancer/testis antigen 68 (CT68), is a germ cell-specific RNA-binding protein that is essential for spermatogenesis and male fertility. It is involved in the regulation of gene expression during meiosis . It has been shown to bind to and stabilise Cdx2 mRNA in early mouse embryos . RBM46 contains two well-defined and one degenerated RNA recognition motifs (RRMs) and a C-terminal double-stranded RNA binding motif (DSRM) .
DUS2, double-stranded RNA binding domain (DUS2_DSRM)
Type: Domain

Dihydrouridine synthases (Dus) is a large family of flavoenzymes comprising eight subfamilies. They catalyse the NADPH-dependent synthesis of dihydrouridine, a modified base found in the D-loop of most tRNAs. Mainly, they contain two functional conserved domains, an N-terminal catalytic domain (TBD) adopting a TIM barrel fold and a unique C-terminal helical domain (HD) devoted to tRNA recognition. However, DUS2 is distinguished from its paralogues and its fungi orthologues by the acquisition of an additional domain, a double stranded RNA binding domain (dsRBD), which serves as the main tRNA binding module .

This entry represents the double stranded RNA binding domain of DUS2 .
Staufen 2, second double-stranded RNA binding domain (STAU2_DSRM_2)
Type: Domain

Staufen 2 is an RNA-binding protein required for the microtubule-dependent transport of neuronal RNA from the cell body to the dendrite . Staufen 2 contains five double-stranded RNA binding motifs (DSRMs).

This entry represents the second DSRM of Staufen 2.
PRKRA, first double-stranded RNA binding domain (PRKRA_DSRM_1)
Type: Domain

Interferon-inducible double-stranded RNA-dependent protein kinase activator A (PRKRA), also known as PACT or RAX, acts as an activator of PKR (the IFN-induced double-stranded RNA-dependent protein kinase) in response to diverse stress signals, such as serum starvation, and peroxide or arsenite treatment . It is an important regulator of PKR dependent signalling pathways in the absence of viral infections . It is also required for siRNA production by DICER1 and for subsequent siRNA-mediated post-transcriptional gene silencing .

PRKRA contains three double-stranded RNA binding motifs (DSRMs). This entry represents the first DSRM of PRKRA.
PRKRA, second double-stranded RNA binding domain (PRKRA_DSRM_2)
Type: Domain

Interferon-inducible double-stranded RNA-dependent protein kinase activator A (PRKRA), also known as PACT or RAX, acts as an activator of PKR (the IFN-induced double-stranded RNA-dependent protein kinase) in response to diverse stress signals, such as serum starvation, and peroxide or arsenite treatment . It is an important regulator of PKR dependent signalling pathways in the absence of viral infections . It is also required for siRNA production by DICER1 and for subsequent siRNA-mediated post-transcriptional gene silencing .

PRKRA contains three double-stranded RNA binding motifs (DSRMs). This entry represents the second DSRM of PRKRA.
PRKRA, third double-stranded RNA binding domain (PRKRA_DSRM_3)
Type: Domain

Interferon-inducible double-stranded RNA-dependent protein kinase activator A (PRKRA), also known as PACT or RAX, acts as an activator of PKR (the IFN-induced double-stranded RNA-dependent protein kinase) in response to diverse stress signals, such as serum starvation, and peroxide or arsenite treatment . It is an important regulator of PKR dependent signalling pathways in the absence of viral infections . It is also required for siRNA production by DICER1 and for subsequent siRNA-mediated post-transcriptional gene silencing .

PRKRA contains three double-stranded RNA binding motifs (DSRMs). This entry represents the third DSRM of PRKRA.
TRBP2 , first double-stranded RNA binding domain (TRBP2_DSRM_1)
Type: Domain

TRBP2 was first identified as a HIV-1 TAR RNA-binding protein . TRBP2 is a component of the RISC loading complex (RLC), which functions in RNA-mediated gene silencing (RNAi). It is a double-stranded RNA (dsRNA)-binding protein that associates with endonuclease Dicer, which cleaves precursor RNA molecules to produce microRNAs (miRNAs) and short interfering RNAs (siRNAs) in RNAi pathway . Together with another dsRNA-binding protein, PACT, they function as key regulators of miRNA and siRNA biogenesis by Dicer in substrate recognition, binding, processing and RISC loading .

TRBP2 contains three double-stranded RNA binding motifs (DSRMs). This entry represents the first DSRM of TRBP2.
TRBP2 , second double-stranded RNA binding domain (TRBP2_DSRM_2)
Type: Domain

TRBP2 was first identified as a HIV-1 TAR RNA-binding protein . TRBP2 is a component of the RISC loading complex (RLC), which functions in RNA-mediated gene silencing (RNAi). It is a double-stranded RNA (dsRNA)-binding protein that associates with endonuclease Dicer, which cleaves precursor RNA molecules to produce microRNAs (miRNAs) and short interfering RNAs (siRNAs) in RNAi pathway . Together with another dsRNA-binding protein, PACT, they function as key regulators of miRNA and siRNA biogenesis by Dicer in substrate recognition, binding, processing and RISC loading .

TRBP2 contains three double-stranded RNA binding motifs (DSRMs). This entry represents the second DSRM of TRBP2.
TRBP2 , third double-stranded RNA binding domain (TRBP2_DSRM_3)
Type: Domain

TRBP2 was first identified as a HIV-1 TAR RNA-binding protein . TRBP2 is a component of the RISC loading complex (RLC), which functions in RNA-mediated gene silencing (RNAi). It is a double-stranded RNA (dsRNA)-binding protein that associates with endonuclease Dicer, which cleaves precursor RNA molecules to produce microRNAs (miRNAs) and short interfering RNAs (siRNAs) in RNAi pathway . Together with another dsRNA-binding protein, PACT, they function as key regulators of miRNA and siRNA biogenesis by Dicer in substrate recognition, binding, processing and RISC loading .

TRBP2 contains three double-stranded RNA binding motifs (DSRMs). This entry represents the third DSRM of TRBP2.
STRBP, first double-stranded RNA binding domain (STRBP_DSRM_1)
Type: Domain

Spermatid perinuclear RNA-binding protein (STRBP, SPNR) is a microtubule-associated RNA-binding protein that localises to the manchette, a rod-like structure composed of microtubules, in developing spermatids. It plays an important role in normal spermatogenesis and sperm function . SPNR is highly expressed in testis, ovary, and brain. It contains two dsRNA binding domains (DRBDs) toward its carboxyl terminus as well as a putative leucine zipper motif .

This entry represents the first double-stranded RNA binding domain of STRBP.
Staufen 2, third double-stranded RNA binding domain (STAU2_DSRM_3)
Type: Domain

Staufen 2 is an RNA-binding protein required for the microtubule-dependent transport of neuronal RNA from the cell body to the dendrite . Staufen 2 contains five double-stranded RNA binding motifs (DSRMs).

This entry represents the third DSRM of Staufen 2.
Staufen 2, fourth double-stranded RNA binding domain (STAU2_DSRM_4)
Type: Domain

Staufen 2 is an RNA-binding protein required for the microtubule-dependent transport of neuronal RNA from the cell body to the dendrite . Staufen 2 contains five double-stranded RNA binding motifs (DSRMs).

This entry represents the fourth DSRM of Staufen 2.
Staufen 1, third double-stranded RNA binding domain (STAU1_DSRM_3)
Type: Domain

Staufen 1 may play a role in specific positioning of mRNAs at given sites in the cell by cross-linking cytoskeletal and RNA components, and in stimulating their translation at the site. It binds double-stranded RNA (regardless of the sequence) and tubulin . It also plays a role in virus particles production of many viruses including of HIV-1, HERV-K, ebola virus and influenza virus .

This entry represents the third DSRM of Staufen 21.
Staufen 2, first double-stranded RNA binding domain (STAU2_DSRM_1)
Type: Domain

Staufen 2 is an RNA-binding protein required for the microtubule-dependent transport of neuronal RNA from the cell body to the dendrite . Staufen 2 contains five double-stranded RNA binding motifs (DSRMs).

This entry represents the first DSRM of Staufen 2.
D-threo-aldose 1-dehydrogenase-like (FDH-like)
Type: Family

L-fucose dehydrogenase (FDH), also known as D-threo-aldose 1-dehydrogenase, catalyses the oxidation of L-fucose to L-fuconolactone in the presence of NADP. It is also active against L-galactose and, to a much lesser degree, D-arabinose. Uses NADP as a hydrogen acceptor much more efficiently than NAD .
Pyridoxal 4-dehydrogenase-like (Pld1-like)
Type: Family

Microbacterium luteolum PLD is a founding member of aldo-keto reductase family 15 member A1 (AKR15A1). It catalyses the irreversible oxidation of pyridoxal .
L-galactose dehydrogenase-like (LGALDH-like)
Type: Family

This entry represents a group of L-galactose dehydrogenase and related proteins, including At-GalDH (At4g33670) from Arabidopsis. At-GalDH catalyses the oxidation of L-galactose to L-galactono-1,4-lactone in the presence of NAD. It uses NAD as a hydrogen acceptor much more efficiently than NADP .
D-arabinose 1-dehydrogenase Ara2-like (Ara2-like)
Type: Family

This entry includes Ara2 and related proteins from fungi. Ara2 catalyses the the oxidation of D-arabinose to D-arabinono-1,4-lactone in the presence of NAD .
Aldo-keto reductase family 1 member A1 (AKR1A)
Type: Family

This entry represents aldo-keto reductase family 1 member A1 (AKR1A), including aldehyde reductase (ALR) from mammals . The AKR1A family belongs to the aldo-keto reductase (AKR) family.

ALR, also known as aldehyde reductase, or ALDR1, catalyses the NADPH-dependent reduction of a variety of aromatic and aliphatic aldehydes to their corresponding alcohols. In vitro substrates include succinic semialdehyde, 4-nitrobenzaldehyde, 1,2-naphthoquinone, methylglyoxal, and D-glucuronic acid .

In general, the aldo-keto reductase (AKR) protein superfamily members reduce carbonyl substrates such as: sugar aldehydes, keto-steroids, keto-prostaglandins, retinals, quinones, and lipid peroxidation by-products . However, there are some exceptions, such as the reduction of steroid double bonds catalysed by AKR1D enzymes (5beta-reductases); and the oxidation of proximate carcinogen trans-dihydrodiol polycyclic aromatic hydrocarbons; while the beta-subunits of potassium gated ion channels (AKR6 family) control Kv channel opening .

Structurally, they contain an (α/β)8-barrel motif, display large loops at the back of the barrel which govern substrate specificity, and have a conserved cofactor binding domain. The binding site is located in a large, deep, elliptical pocket in the C-terminal end of the β-sheet, the substrate being bound in an extended conformation. The hydrophobic nature of the pocket favours aromatic and apolar substrates over highly polar ones . They catalyse an ordered bi bi kinetic mechanism in which NAD(P)H cofactor binds first and leaves last . Binding of the NADPH coenzyme causes a massive conformational change, reorienting a loop, effectively locking the coenzyme in place. This binding is more similar to FAD- than to NAD(P)-binding oxidoreductases .
Aldo-keto reductase family 1 member C (AKR1C)
Type: Family

This entry represents aldo-keto reductase family 1 member C (AKR1C), including aldehyde reductase (ALR) AKR1C1-5 from mammals. The AKR1C family belongs to the aldo-keto reductase (AKR) family.

ALR, also known as aldehyde reductase, or ALDR1, catalyses the NADPH-dependent reduction of a variety of aromatic and aliphatic aldehydes to their corresponding alcohols. In vitro substrates include succinic semialdehyde, 4-nitrobenzaldehyde, 1,2-naphthoquinone, methylglyoxal, and D-glucuronic acid .

In general, the aldo-keto reductase (AKR) protein superfamily members reduce carbonyl substrates such as: sugar aldehydes, keto-steroids, keto-prostaglandins, retinals, quinones, and lipid peroxidation by-products . However, there are some exceptions, such as the reduction of steroid double bonds catalysed by AKR1D enzymes (5beta-reductases); and the oxidation of proximate carcinogen trans-dihydrodiol polycyclic aromatic hydrocarbons; while the beta-subunits of potassium gated ion channels (AKR6 family) control Kv channel opening .

Structurally, they contain an (α/β)8-barrel motif, display large loops at the back of the barrel which govern substrate specificity, and have a conserved cofactor binding domain. The binding site is located in a large, deep, elliptical pocket in the C-terminal end of the β-sheet, the substrate being bound in an extended conformation. The hydrophobic nature of the pocket favours aromatic and apolar substrates over highly polar ones . They catalyse an ordered bi bi kinetic mechanism in which NAD(P)H cofactor binds first and leaves last . Binding of the NADPH coenzyme causes a massive conformational change, reorienting a loop, effectively locking the coenzyme in place. This binding is more similar to FAD- than to NAD(P)-binding oxidoreductases .
Aldo-keto reductase family 1 member D1 (AKR1D1)
Type: Family

This entry represents aldo-keto reductase family 1 member D1 (AKR1D1). It catalyses the stereospecific NADPH-dependent reduction of the C4-C5 double bond of bile acid intermediates and steroid hormones carrying a delta-4-3-one structure to yield an A/B cis-ring junction. This cis-configuration is crucial for bile acid biosynthesis and plays important roles in steroid metabolism . It is capable of reducing a broad range of delta-4-3-ketosteroids from C18 (such as, 17beta-hydroxyestr-4-en-3-one) to C27 (such as, 7alpha-hydroxycholest-4-en-3-one) .

In general, the aldo-keto reductase (AKR) protein superfamily members reduce carbonyl substrates such as: sugar aldehydes, keto-steroids, keto-prostaglandins, retinals, quinones, and lipid peroxidation by-products . However, there are some exceptions, such as the reduction of steroid double bonds catalysed by AKR1D enzymes (5beta-reductases); and the oxidation of proximate carcinogen trans-dihydrodiol polycyclic aromatic hydrocarbons; while the beta-subunits of potassium gated ion channels (AKR6 family) control Kv channel opening .

Structurally, they contain an (α/β)8-barrel motif, display large loops at the back of the barrel which govern substrate specificity, and have a conserved cofactor binding domain. The binding site is located in a large, deep, elliptical pocket in the C-terminal end of the β-sheet, the substrate being bound in an extended conformation. The hydrophobic nature of the pocket favours aromatic and apolar substrates over highly polar ones . They catalyse an ordered bi bi kinetic mechanism in which NAD(P)H cofactor binds first and leaves last . Binding of the NADPH coenzyme causes a massive conformational change, reorienting a loop, effectively locking the coenzyme in place. This binding is more similar to FAD- than to NAD(P)-binding oxidoreductases .
Aldo-keto reductase family 1 member E2 (AKR1E2)
Type: Family

This entry represents aldo-keto reductase family 1 member E2 (AKR1E2), which catalyses the NADPH-dependent reduction of 1,5-anhydro-D-fructose (AF) to 1,5-anhydro-D-glucitol . AKR1E2 is a testis aldo-keto reductase (tAKR), which is also known as testis-specific protein (TSP), or LoopADR .

In general, the aldo-keto reductase (AKR) protein superfamily members reduce carbonyl substrates such as: sugar aldehydes, keto-steroids, keto-prostaglandins, retinals, quinones, and lipid peroxidation by-products . However, there are some exceptions, such as the reduction of steroid double bonds catalysed by AKR1D enzymes (5beta-reductases); and the oxidation of proximate carcinogen trans-dihydrodiol polycyclic aromatic hydrocarbons; while the beta-subunits of potassium gated ion channels (AKR6 family) control Kv channel opening .

Structurally, they contain an (α/β)8-barrel motif, display large loops at the back of the barrel which govern substrate specificity, and have a conserved cofactor binding domain. The binding site is located in a large, deep, elliptical pocket in the C-terminal end of the β-sheet, the substrate being bound in an extended conformation. The hydrophobic nature of the pocket favours aromatic and apolar substrates over highly polar ones . They catalyse an ordered bi bi kinetic mechanism in which NAD(P)H cofactor binds first and leaves last . Binding of the NADPH coenzyme causes a massive conformational change, reorienting a loop, effectively locking the coenzyme in place. This binding is more similar to FAD- than to NAD(P)-binding oxidoreductases .