SII-SWORD/CoKE huggingface dataset:
Dynein axonemal assembly factor 5, HEAT-repeat domain (HEAT_DAAF5)
Type: Domain

This entry represents a domain found in the central region of Dynein axonemal assembly factor 5 (DAAF5) from animals, which consists of HEAT repeats.

DAAF5 is a cytoplasmic protein involved in the delivery of the dynein machinery to the motile cilium. It is required for the assembly of the axonemal dynein inner and outer arms, two structures attached to the peripheral outer doublet A microtubule of the axoneme, that play a crucial role in cilium motility .
DAAF9, N-terminal domain (DAAF9_N)
Type: Domain

This domain is found N-terminal in human DAAF9 and related proteins. It shares similarity with the aminopeptidase P domain of Spt16, a core component of the histone chaperone FACT. These domains likely share the same α/β fold with Ribonuclease H-like motif.

Dynein axonemal assembly factor 9 DNAAF9 (Shulin) is a dynein axonemal assembly factor that regulates the transport and activation of outer dynein arms (ODAs) in cilia. It binds and inhibits ODAs in the cytoplasm, maintaining them in a closed conformation until they are delivered to cilia. It may interact with ARL-3. This GTP-dependent interaction might ensure spatiotemporal control of dynein function, critical for proper ciliary beating in multiciliated cells such as airway epithelia. Dysregulation of DNAAF9 is linked to primary ciliary dyskinesia (PCD), characterised by impaired mucociliary clearance and respiratory defects .
HPS5-like, beta-propeller domain (Beta-prop_HPS5-like)
Type: Domain

This entry represents the β-propeller domain found in HPS5, a component of the biogenesis of lysosome-related organelles complex-2 (BLOC-2) and which has a role in the endo-lysosomal dynamics of skin fibroblasts . Its mutation or absence has been linked to eye-colour mutations in insects and Hermansky-Pudlak type 5 syndrome (HPS-5) in mammals, a disease characterised by defects in lysosome-related organelles such as melanosomes and platelet dense granules . This entry also represents the N-terminal β-propeller domain found in the tectonin β-propeller repeat-containing protein 2 (TCPR2), which is a paralogue of HPS5. TCPR2 acts as a molecular scaffold linking early secretion pathway and autophagy as it associates with several trafficking components, among them the COPII coat protein SEC24D. It is required for stabilisation of SEC24D protein levels, maintenance of functional ER exit sites (ERES), and efficient ER export in a manner dependent on binding to lipidated LC3C .
HRPKS sdrA-like, NAD(P)-binding domain (NAD-bd_HRPKS_sdrA)
Type: Domain

This domain is found in Highly reducing polyketide synthase srdA from Neurospora crassa (HRPKS sdrA) and similar fungal proteins. HRPKS sdrA is part of the gene cluster that mediates the biosynthesis of sordarial, a salicylic aldehyde structurally related to the phytotoxin pyriculol . This domain is predicted to adopt a Rossmann-type fold.
KIAA0319-like, C-terminal domain (KIAA0319-like_C)
Type: Domain

This domain is found in human Dyslexia-associated protein KIAA0319 and related animal proteins. KIAA0319 is involved in neuronal migration during development of the cerebral neocortex. This protein probably function in a cell autonomous and a non-cell autonomous manner and plays a role in appropriate adhesion between migrating neurons and radial glial fibers . This domain is found C-terminal and it is predicted to adopt an α/β structure with some similarity to NOTCH heterodimerisation domain.
Dystrophin-1-like, spectrin repeat domain (Spectrin_Dys-1)
Type: Domain

This domain is found in Dystrophin-1 from Caenorhabditis elegans (Dys-1) and similar worm sequences. Dys-1 plays a role in cholinergic transmission and as a functional partner of dystrobrevin (Dyb-1), necessary for muscle maintenance. It is required for neuronal positioning .
HVO_0163, N-terminal HTH domain (HTH_HVO_0163_N)
Type: Domain

This HTH domain is found at the N-terminal of the ArsR family transcription regulator HVO_0163 (

) from Haloferax volcanii and similar archaeal sequences.
HVO_0234-like, beta-propeller (Beta-prop_HVO_0234)
Type: Domain

This family represents a group of proteins mainly from halobacteria, including HVO_0234 from Haloferax volcanii (

). Members are predicted to adopt a β-propeller fold.
iHD-CE (iHD-CE)
Type: Domain

This entry represents an inactive HD-CE domain (iHD-CE) which acts as a sensor in the antiviral immunity systems and it is predominantly located within HSP90 systems. Specifically, it is associated with wHTH repeats located at the C-terminal (

) .
wHTH-Hsp90, Na associated (wHTH-HSP90_Na-assoc)
Type: Domain

This is a wHTH domain commonly observed in tandem repeats with 5 or more modules and located at the C-terminal of HSP90 proteins engaged in antiviral immunity. These proteins often additionally feature an inactive HD-CE domain (

) at the N-terminal. Structural modelling suggests that the wHTH repeats form a ring-shaped module for recognising nucleic acids .
Hydroxyproline O-arabinosyltransferase-like domain (HPAT-like)
Type: Domain

The Hydroxyproline O-arabinosyltransferase family is comprised of glycosyltransferases involved in the post-translational modification of plant proteins. Members of this family catalyse the transfer of L-arabinose to the hydroxyl group of hydroxyproline (Hyp) residues in target proteins, such as extensins and small signalling peptides. This modification is crucial for the proper function of these proteins, which play roles in plant structure and signalling. In legumes, some family members are also implicated in the autoregulation of nodulation (AON), a process that controls the number of root nodules formed in response to nitrogen availability and rhizobial colonisation. They function upstream of receptor kinases like SUNN and through CLE peptides to regulate long-distance signalling events between the root and shoot .

This domain is also found in SERGT1, also known as AtSGT1, a peptidyl serine O-alpha-galactosyltransferase .
Imm33-like domain (Imm33-like)
Type: Domain

This entry represents a family of bacterial proteins that are structurally related to the Imm33 family of putative immunity proteins.
Immunity protein WapI-like (WapI)
Type: Family

The WapI family comprises immunity proteins that are part of a toxin-immunity protein module functioning as a cellular contact-dependent growth inhibition (CDI) system. These proteins neutralize the tRNase activity of their cognate toxin WapA upon expression in E.coli . Notably, they do not inhibit WapA from other strains of Bacillus subtilis. The WapA C-terminal cannot be expressed independently in E.coli, but can be cloned when its cognate immunity protein gene is present. The structure of these proteins resembles the fold of the Whirly ssDNA binding proteins.
Increased DNA methylation 1, C-terminal (IDM1_C)
Type: Domain

This domain is found at the C-terminal end of Increased DNA methylation 1 (IDM1) from Arabidopsis thaliana and similar plant proteins. IDM1 is a histone H3 acetyltransferase that binds methylated DNA at chromatin sites lacking histone H3K4 di- or trimethylation and catalyses H3K18 and H3K23 acetylation . It is also required for ROS1-mediated DNA demethylation .
Putative E3 ubiquitin-protein ligase LIN, N-terminal domain (LIN_N)
Type: Domain

This region is found towards the N-terminal end in a group of plant proteins, including the putative E3 ubiquitin-protein ligase LIN from Medicago truncatula. This domain is predicted to consist of ARM-like repeats.

E3 ubiquitin-protein ligase LIN is involved in the rhizobial infection process . This protein plays an important role in the early steps of bacterial symbiont thread formation in roots, and in growth, differentiation and maintenance of nodules .
INO80 complex subunit F (INO80F)
Type: Domain

This entry represents the helical region from INO80 subunit F (also known as TCF3 fusion partner, TFTP or amida) from vertebrates and its orthologues from fungi, including S. pombe Hap2 (

) and Ino80 complex HMG box subunit Nht1 (

). It plays an important role in p53-independent cellular apoptosis and it also plays a role in cell arrest and spermatogenesis . It is likely a regulatory component of the chromatin remodelling INO80 complex .
Putative E3 ubiquitin-protein ligase LIN, ARM repeats domain (ARM_LIN_2nd)
Type: Domain

This region of armadillo-like repeats is found in a group of plant proteins, including the putative E3 ubiquitin-protein ligase LIN from Medicago truncatula. This entry is often found C-terminal to

and N-terminal to

.

E3 ubiquitin-protein ligase LIN is involved in the rhizobial infection process . This protein plays an important role in the early steps of bacterial symbiont thread formation in roots, and in growth, differentiation and maintenance of nodules .
INO80 complex subunit E, N-terminal (INO80E_N)
Type: Domain

INO80 complex subunit E (INO80E) is specific to metazoan . It is a putative regulatory component of the chromatin remodeling INO80 complex, which is involved in transcriptional regulation, DNA replication and probably DNA repair . Human INO80E is the orthologue of INO80 complex subunit 3 (Iec3) from S.pombe, however, they are represented in different models (

). This entry represents the helical region found at the N-terminal end.
Integrator complex subunit 7, N-terminal (INTS7_N)
Type: Domain

This entry represents the superhelical α-solenoid found at the N-terminal of INTS7.

Integrator complex subunit 7 (INTS7) is a component of the integrator complex which is recruited to the U1 and U2 snRNA genes and mediates the snRNAs' 3' end processing. The integrator complex interacts with the C-terminal tail of the largest subunit of RNA-polymerase II to promote 3'-snRNA processing . INTS7 interacts with INTS1 and INTS2 making extensive contacts with each other, nucleating the assembly of the whole INTAC complex . In zebrafish, C. elegans and Drosophila, INTS7 has been found to be essential for normal development .
Integrator complex subunit 7, helical bundle (INTS7_HB)
Type: Domain

This entry represents the helical bundle (HB) of INTS7, localised between the superhelical α-solenoid (

) and the C-terminal β-sandwich (

) .

Integrator complex subunit 7 (INTS7) is a component of the integrator complex which is recruited to the U1 and U2 snRNA genes and mediates the snRNAs' 3' end processing. The integrator complex interacts with the C-terminal tail of the largest subunit of RNA-polymerase II to promote 3'-snRNA processing . INTS7 interacts with INTS1 and INTS2 making extensive contacts with each other, nucleating the assembly of the whole INTAC complex . In zebrafish, C. elegans and Drosophila, INTS7 has been found to be essential for normal development .
Ints3-like, C-terminal (HEAT_Ints3_C)
Type: Domain

This is the C-terminal domain of human Integrator complex subunit 3 (Ints3) and its homologues. Ints3 is a component of the Integrator (INT) complex, which is involved in the small nuclear RNAs (snRNA) U1 and U2 transcription and in their 3'-box-dependent processing. This domain forms a dimer, which binds single-stranded RNA/DNA . This domain consists of HEAT repeats.
KANSL3, helical domain (KANSL3_1st)
Type: Domain

This domain is found in human KAT8 regulatory NSL complex subunit 3 (KANSL3) and its homologues. KANSL3 is a non-catalytic component of the NSL histone acetyltransferase complex, a multiprotein complex that mediates histone H4 acetylation at 'Lys-5'- and 'Lys-8' (H4K5ac and H4K8ac) at transcription start sites and promotes transcription initiation . The NSL complex also acts as a regulator of gene expression in mitochondria . Within the NSL complex, KANSL3 is required to promote KAT8 association with mitochondrial DNA . This domain is predicted to adopt a globular structure consisting of array of eight helices.
KDM8, N-terminal (ARM_KDM8_N)
Type: Domain

This entry represents the N-terminal domain of human Bifunctional peptidase and arginyl-hydroxylase JMJD5 (also known as KDM8) and similar proteins, which consists of ARM repeats. KDM8 functions both as an endopeptidase and 2-oxoglutarate-dependent monooxygenase .
E3 ubiquitin-protein ligase MARCHF6-like, C-terminal domain (MARCHF6-like_C)
Type: Domain

This domain is found at the C-terminal end of human E3 ubiquitin-protein ligase MARCHF6, its homologue in Schizosaccharomyces pombe Doa10 and similar eukaryotic sequences. MARCHF6 promotes 'Lys-48'-linked ubiquitination of target proteins, leading to their proteasomal degradation . This domain is predicted to adopt an all α-helical structure.
Uncharacterized bromodomain-containing protein 10, helical domain (KIAA2026_hel)
Type: Domain

This entry represents an helical domain found in the uncharacterised bromodomain-containing protein 10 (BRD10, also known as KIAA2026) humans and similar sequences, whose function is currently unknown. This domain is found towards the N-terminal end and may adopt an all-helical structure.
KIF14, four-helical bundle (4HB_KIF14)
Type: Domain

This is a four helical bundle domain (4HB) found in Kinesin-like protein KIF14, a microtubule motor protein that binds to microtubules with high affinity through each tubulin heterodimer and has an ATPase activity. It plays a role in many processes like cell division, cytokinesis and also in cell proliferation and apoptosis .
Kinesin-like protein KIF6/9, C-terminal (KIF6/9_C)
Type: Domain

This entry represents a region found at the C-terminal of Kinesin-like protein KIF6 and 9 from animals and KIF1 from Chlamydomonas reinhardtii. KIF9 is essential for normal male fertility and for progressive motility of spermatozoa. This region, which is predicted to form two long α-helices, is often found associated with

.
HVO_1552, C-terminal (HVO_1552_C)
Type: Domain

This domain is found at the C-terminal of the predicted ArsR family transcription regulator HVO_1552 (

) from Haloferax volcanii and similar archaeal sequences. It is predicted to adopt an α-helical structure.
HVO_1752, TRASH domain (TRASH_HVO_1752)
Type: Domain

This TRASH domain is found at the C-terminal of the predicted Lrp/AsnC family transcription regulator HVO_1752 (

) from Haloferax volcanii and similar archaeal proteins.
E3 ubiquitin-protein ligase RFWD3-like, WD40 domain (WD40_RFWD3)
Type: Domain

This entry represents the WD40-repeat (WDR) domain of the E3 ubiquitin-protein ligase RFWD3, a protein required for the repair of DNA interstrand cross-links (ICL) in response to DNA damage . This domain is responsible for the functional interactions that allow RFWD3 to maintain genomic stability .
HVO_2833, C-terminal (HVO_2833_C)
Type: Domain

This is the C-terminal domain of the predicted ArsR family transcription regulator HVO_2833 (

) from Haloferax volcanii. Its specific function is unknown.
HVO_2928, N-terminal (HVO_2928_N)
Type: Domain

This domain is found at the N-terminal of the predicted transcription regulator HVO_2928 (

) from Haloferax volcanii and similar proteins from Halobacteria. This domain is predicted to adopt an α-β structure. It is often found associated with

.
E3 ubiquitin-protein ligase UBR4-like domain (UBR4-like_dom)
Type: Domain

This domain is found in human E3 ubiquitin-protein ligase UBR4 and similar proteins found in eukaryotes. UBR4 is a component of the N-end rule pathway. It recognises and binds to proteins bearing specific N-terminal residues that are destabilising according to the N-end rule, leading to their degradation .
HVO_A0563, N-terminal (HVO_A0563_N)
Type: Domain

This domain is found at the N-terminal of the predicted transcription regulator HVO_A0563 (

) from Haloferax volcanii and similar archaeal proteins. This domain is predicted to adopt an α-β structure. It is often found associated with

.
KIF21A/B, second helical domain (KIF21A/B_hel_2)
Type: Domain

This domain is found towards the C-terminal of human Kinesin-like protein KIF21A/B and similar eukaryotic sequences. KIF21A is a processive microtubule plus-end directed motor protein involved in neuronal axon guidance. It is recruited by KANK1 to cortical microtubule stabilising complexes (CMSCs) at focal adhesions (FAs) rims where it promotes microtubule capture and stability. It controls microtubule polymerisation rate at axonal growth cones and suppresses microtubule growth without inducing microtubule disassembly once it reaches the cell cortex . Mutations in this protein are associated with ocular abnormalities. This domain, which is found associated to

and

, folds into two long α-helices .

Klp12, the orthologue from C. elegans, is a microtubule-binding motor protein which has ATPase activity . It forms a complex with alpha and beta tubulins, and preferentially binds to the growing microtubule plus-end to stabilise it and detaches following ATP hydrolysis . It negatively regulates axonal length through inhibiting microtubule polymerisation at its plus-end .
KIF21A/B, first helical domain (KIF21A/B_hel_1)
Type: Domain

This domain is found in human Kinesin-like protein KIF21A/B and similar eukaryotic sequences. KIF21A is a processive microtubule plus-end directed motor protein involved in neuronal axon guidance. It is recruited by KANK1 to cortical microtubule stabilising complexes (CMSCs) at focal adhesions (FAs) rims where it promotes microtubule capture and stability. It controls microtubule polymerisation rate at axonal growth cones and suppresses microtubule growth without inducing microtubule disassembly once it reaches the cell cortex . Mutations in this protein are associated with ocular abnormalities. This domain, which is found associated to

,

and

, is predicted to fold into two long α-helices.
NWD2, C-terminal beta-propeller domain (Beta-prop_NWD2_C)
Type: Domain

This entry represents the β-propeller domain found at the C-terminal of NACHT and WD repeat domain-containing protein 2 (NWD2) from human and similar proteins. The function of these proteins is not yet known.
NUP160, middle TPR domain (TPR_NUP160_M)
Type: Domain

This entry represents a segment of TPRs found in the middle region of nucleoporin Nup160 from animal and plants, as well as in the homologues from fungi. NUP160 depletion could restore autophagy and inhibit fibrosis and inflammatory response in high glucose-treated . The Arabidopsis Nup160, a scaffold Nup, is important for regulating the floral transition, a key developmental phase change in flowering plants, through modulating the subcellular localisation of HOS1 at NPCs .

NUP160 is one of up to 60 proteins that constitute the Nuclear Pore Complex (NPC) as a component of the NUP107-160 subcomplex . NUP160, in conjunction with NUP133, interacts with NUP98 and NUP153, mediating mRNA export . NUP160 depletion could restore autophagy and inhibit fibrosis and inflammatory response in high glucose-treated . NUP160 mutations have been associated with Steroid-Resistant Nephrotic Syndrome (SRNS). Silencing Drosophila NUP160 specifically in nephrocytes results in functional abnormalities, reduced cell size and nuclear volume, as well as a disorganised nuclear membrane structure .
NUP160, C-terminal TPR domain (TPR_NUP160_C)
Type: Domain

This entry represents the TPR-like repeats domain found in the C-terminal region of nucleoporin Nup160. The Arabidopsis Nup160, a scaffold Nup, is important for regulating the floral transition, a key developmental phase change in flowering plants, through modulating the subcellular localisation of HOS1 at NPCs .

NUP160 is one of up to 60 proteins that constitute the Nuclear Pore Complex (NPC) as a component of the NUP107-160 subcomplex . NUP160, in conjunction with NUP133, interacts with NUP98 and NUP153, mediating mRNA export . NUP160 depletion could restore autophagy and inhibit fibrosis and inflammatory response in high glucose-treated . NUP160 mutations have been associated with Steroid-Resistant Nephrotic Syndrome (SRNS). Silencing Drosophila NUP160 specifically in nephrocytes results in functional abnormalities, reduced cell size and nuclear volume, as well as a disorganised nuclear membrane structure .
ArlX (ArlX)
Type: Family

This entry represents ArlX (also known as FlaX), a component of the Sulfolobus motility machinery (archaellum) . This protein is conserved in crenarchaeal archaella and forms ring-shaped oligomers. Its C-terminal region interacts with ArlI (FlaI), the archaellum motor ATPase that is involved in assembly and rotation of the archaellum .
NuiA-like (NuiA-like)
Type: Family

This entry represents a group of fungal proteins that are related to the nuclease A inhibitor NuiA (

). NuiA is known to regulate the activity of NucA, one of the most potent nucleases involved in degradation of both single- and double-stranded DNA and RNA. The NucA inhibition by NuiA involves an unusual divalent metal ion bridge that connects the nuclease with its inhibitor. A highly conserved glutamate extends into the active site, mimicking the charge of a phosphate. The functionally essential glutamate is conserved within this family. In some members, it is replaced with aspartate. Most members of this family bear a deletion affecting the second interaction site located on one of the two 'jaws' of the NuiA structure and known to contribute to the specificity and strength of the NuiA-NucA interaction. The lack of this region indicates some functional differences of this group of potential inhibitors.
Nucleoporin POM152, N-terminal transmembrane domain (TMD_POM152)
Type: Domain

This domain is found at the N-terminal of Nucleoporin POM152 from Saccharomyces cerevisiae and similar fungal proteins.

POM152 functions as a component of the nuclear pore complex (NPC) . This protein consists of an N-terminal transmembrane domain (TMD) and an extended C-terminal domain (CTD) with tandem repeats of Ig-like domains .
Nucleoporin POM152, Ig-like domain (Ig-like_POM152)
Type: Domain

This entry includes the third and sixth Ig-like domains found in Nucleoporin POM152 from yeast, a component of the nuclear pore complex (NPC) .

POM152 functions as a component of the nuclear pore complex (NPC) . This protein consists of an N-terminal transmembrane domain (TMD) and an extended C-terminal domain (CTD) with tandem repeats of Ig-like domains .
Nucleoporin POM152, first Ig-like domain (Ig-like_POM152_1st)
Type: Domain

This is the first immunoglobulin-like (Ig-like) domain found in Nucleoporin POM152 from yeast and similar fungal proteins.

POM152 functions as a component of the nuclear pore complex (NPC) . This protein consists of an N-terminal transmembrane domain (TMD) and an extended C-terminal domain (CTD) with tandem repeats of Ig-like domains .
Nucleoporin POM152, ninth Ig-like domain (Ig-like_POM152_9th)
Type: Domain

This domain is found in Nucleoporin POM152 from yeast and similar fungal proteins. This domain is predicted to adopt an immunoglobulin-like structure and it is the ninth in the tandem.

POM152 functions as a component of the nuclear pore complex (NPC) . This protein consists of an N-terminal transmembrane domain (TMD) and an extended C-terminal domain (CTD) with tandem repeats of Ig-like domains .
Nucleoporin POM152, immunoglobulin-like domain (Ig_POM152)
Type: Domain

This domain is found in Nucleoporin POM152 from Schizosaccharomyces pombe and similar fungal proteins. This domain is predicted to adopt an immunoglobulin-like structure.

POM152 functions as a component of the nuclear pore complex (NPC) . This protein consists of an N-terminal transmembrane domain (TMD) and an extended C-terminal domain (CTD) with tandem repeats of Ig-like domains .