SII-SWORD/CoKE huggingface dataset:
F54D1.6-like, second Ig-like domain (F54D1_6-like_Ig-like_2)
Type: Domain

This is an immunoglobulin-like domain of the uncharacterised protein F54D1.6 from Caenorhabditis elegans and similar worm sequences. It is often found associated to

and

.
Follistatin-related protein 1, EF-hand domain pair (EF-hand_FSTL1)
Type: Domain

This is the EF-hand domain pair found in human Follistatin -like protein 1 (FSTL1), a secreted glycoprotein involved in angiogenesis, regulation of the immune response, cell proliferation and differentiation . EF-hands tend to occur in pairs or higher copy numbers.
STRA8, bHLH domain (bHLH_STRA8)
Type: Domain

This bHLH domain is found in the family of Stimulated by retinoic acid gene 8 protein (STRA8). This protein is required for the transition into meiosis for both female and male germ cells . In female germ cells, it acts as a key effector of the meiotic program and is required for premeiotic DNA replication and subsequent events in meiotic prophase .
PF0610-like, rubredoxin-like zinc beta-ribbon, C-terminal domain (PF0610-like_Zn_ribbon_C)
Type: Domain

This domain is found C-terminal in PF0610 protein from Pyrococcus furiosus (

) and related homologous proteins. This protein has a Zn-ribbon embedded in winged HTH fold. This entry represents the C-terminal domain, which is composed of a rubredoxin-like zinc beta-ribbon domain with two CXXC sequence elements .

The function of PF0610 has not been fully chracterized. wHTH domains containing proteins are believed to serve as DNA- or RNA-binding domains

. A large number of wHTH proteins are transcriptional regulators, while others are involved in chromosome packing. Because of its apparent sequence-independent interaction with DNA, PF0610 could be a part of the chromatin system of P. furiosus. The numerous basic residues in PF0610 ensure strong DNA interactions. The Zn ribbon motif could help improve the structural stability of the protein at a high temperature. Another possibility is that PF0610 is a metal-dependent transcription factor. This is based on DNA microarray data. However, further research is needed to conclude if PF0610 is an iron-containing protein
Swiss Army Knife protein, DSP-PTPase phosphatase domain (PTP-SAK)
Type: Domain

The Swiss Army Knife class of proteins features a diverse domain repertoire acting to repair RNA damaged in the wake of RNase attacks. PTP-SAK is one such domain, a phosphatase of the rhodanese-phosphatase superfamily. It is predicted to 'clean' RNA ends by removing phosphate groups, preparing them for ligation by their associating RNA ligases .
FORGETTER1, first zinc ribbon domain (Znr_FGT1_1)
Type: Domain

This domain is found in the Arabidopsis FORGETTER1 (FGT1) and related plant proteins. The domain represented by this entry is predicted to adopt a zinc ribbon fold and it is the first of the predicted pair of two.

FGT1 mediates stress-induced chromatin memory by modulating nucleosome occupancy . This protein interacts with chromatin remodelers of the SWI/SNF and ISWI families, which also display reduced heat stress memory. It is the orthologue of metazoan Strawberry notch, a highly conserved co-activator of the developmental regulator Notch.
FORGETTER1, second zinc ribbon domain (Znr_FGT1_2)
Type: Domain

This domain is found in the Arabidopsis FORGETTER1 (FGT1) and related proteins from plants and some bacterial species. It is predicted to adopt a zinc ribbon fold and it is the second of the predicted pair of two.

FGT1 mediates stress-induced chromatin memory by modulating nucleosome occupancy . This protein interacts with chromatin remodelers of the SWI/SNF and ISWI families, which also display reduced heat stress memory. It is the orthologue of metazoan Strawberry notch, a highly conserved co-activator of the developmental regulator Notch.
C2H2-type zinc finger, ascomycetes (Znf-C2H2_ascomycetes)
Type: Domain

This is a presumed C2H2-type zinc finger domain found in a group of uncharacterised proteins from ascomycetes.
Tetratricopeptide repeats region, fungi (TPR_fung)
Type: Domain

This entry represents the predicted tetratricopeptide repeats (TPR) found in a group of uncharacterised fungal proteins, including

from the rose-picker's disease fungus.
Rho GTPase-activating protein 29/45, N-terminal (RHG29_45_N)
Type: Domain

This entry represents a domain found at the N-terminal end of Rho GTPase-activating protein 29 (RHG29) and 45 (RHG45, also known as HMHA1). These proteins are GTPase activators for the Rho-type GTPases. HMHA1 may be able to negatively regulate the actin cytoskeleton as well as cell spreading .
Tetratricopeptide repeats, fungi 2 (TPR_fung_2)
Type: Domain

These predicted tetratricopeptide repeats (TPR) are found in a group of uncharacterised fungal proteins. This domain is often found associated with

.
E3 ubiquitin-protein ligase listerin, tetratricopeptide repeats region (TPR_Rkr-1)
Type: Domain

This region of predicted tetratricopeptide repeats (TPR) is found in E3 ubiquitin-protein ligase listerin from Neurospora crassa (Rkr-1) and similar fungal proteins. Rkr-1 is a component of the ribosome quality control complex (RQC), a ribosome-associated complex that mediates ubiquitination and extraction of incompletely synthesised nascent chains for proteasomal degradation .
SCAF11-like, C-terminal domain (SCAF11-like_C)
Type: Domain

This domain is found at the C-terminal end of human protein SCAF11, SCAF1 and PHD and RING finger domain-containing protein 1. These proteins play a role in pre-mRNA alternative splicing by regulating spliceosome assembly . The SCAF1 C-terminal domain binds to the CTD domain of RNA polymerase II, helping to couple transcription with pre-mRNA splicing. It has an α-helical structure and appears to be important in connecting the processes of making and processing RNA. The function of this domain is particularly relevant in cancer, as SCAF1 is involved in alternative mRNA processing in aggressive ovarian cancers .
MBTPS1, fourth domain (MBTPS1_4th)
Type: Domain

This domain is found in the family of serine proteases such as MBTPS1 and SBT6.1 that are involved in regulated intramembrane proteolysis (RIP) of various substrates, playing a crucial role in cellular signalling and regulation. This domain is predicted to fold into a globular structure with significant similarity to domains belonging to class I glutamine amidotransferase superfamily (

).

MBTPS1 proteases cleave after hydrophobic or small residues, with a preference for Arg or Lys at the P4 position . They are responsible for the proteolytic activation of sterol regulatory element-binding proteins (SREBPs), cyclic AMP-dependent transcription factors (ATF6 and ATF6B), and other factors like BDNF, GNPTAB, and FAM20C . In plants, SBT6.1 participate in stress response signalling and cell wall remodelling by processing factors like BZIP17 and pectinesterases .
Isoleucine--tRNA ligase, cytoplasmic, ubiquitin-like domain (Ubiquitin_IARS1)
Type: Domain

This domain is found in two copies toward the C-terminal end of human Isoleucine--tRNA ligase, cytoplasmic (IARS1) and similar sequences predominantly found in vertebrates. IARS1 catalyses the specific attachment of an amino acid to its cognate tRNA in a 2 step reaction: the amino acid (AA) is first activated by ATP to form AA-AMP and then transferred to the acceptor end of the tRNA. This domain is predicted to adopt an ubiquitin-like fold.
FNG domain (FNG)
Type: Domain

This entry shows a β-sandwich structure that has similarity to known carbohydrate binding domain families CBM61 and CBM70. This domain is found at the N-terminal of proteins that contain repeated domains, suggesting these proteins may act as carbohydrate binding adhesins. This domain contains a conserved FNG sequence after which the domain is named.
FmdE-like, treble clef zinc finger (Znf-Tbcl_FmdE)
Type: Domain

This treble clef zinc finger is found C-terminal in some members of FmdE family that are implicated in microbial methanogenesis, including

from Syntrophus aciditrophicus . This domain follows the α/β core domain (

) and contains four invariant cysteine residues that coordinate the zinc atom.
Endo-acting ulvan lyase, beta-trefoil domain (Beta-tre_PLH30)
Type: Domain

This entry represents the β-trefoil domain found in endo-acting ulvan lyase mainly found in bacteroidota. Ulvan lyases degrade the main polysaccharide component of green seaweed cell walls . This domain binds to ulvan .
TPR repeat domain, actinomycetes (TPR_rep_actino)
Type: Domain

These predicted tetratrico peptide repeats (TPR) are found in a group of uncharacterised proteins from actinomycetes. This entry is found C-terminal to

in some sequences.
FBX41/ZN365, C2H2-type zinc finger (FBX41/ZN365_Znf-C2H2)
Type: Domain

This classical C2H2 zinc finger domain is found in F-box only protein 41 (FBX41) and related proteins. including ZN365. Members of the F-box protein family, such as FBX41, are characterised by an approximately 40-amino acid F-box motif. These proteins are substrate recognition component of the SCF complexes. They interact with SKP1 through the F box, and with ubiquitination targets through other protein interaction domains . ZN365 is involved in homologous recombination repair pathway and contributes to the genomic stability by preventing telomere dysfunction .
F-box protein At5g52880-like, ARM repeats region (At5g52880_ARM)
Type: Domain

This domain is found N-terminal in Arabidopsis thaliana F-box protein At5g52880 and related plant proteins. It usually precedes F-box

.
FAKV Clamp protein (FAKV_Clamp)
Type: Family

This entry represents the Fako virus (FAKV) Clamp protein (

) and related sequences. It folds into a complex α/β structure.
SCAP, N-terminal (SCAP_N)
Type: Domain

This entry represents a domain found at the N-terminal of SCAP (Sterol regulatory element-binding protein cleavage-activating protein) and similar animal proteins. This domain is the luminal domain of SCAP, which binds cholesterol .

SCAP is a key player in the sterol regulatory element-binding protein (SREBP) pathway that controls the cellular homeostasis of sterol . It consists of a luminal domain, eight transmembrane segments from which TM2-TM6 corresponds to the SSD (

) and a WD40 domain at the C-terminal .
SCAP, beta-propeller (Beta-prop_SCAP)
Type: Domain

This entry represents the β-propeller domain found at the C-terminal of SCAP (Sterol regulatory element-binding protein cleavage-activating protein). This domain is involved in the interaction with SREBP . Members of this entry are specific to animals.

SCAP is a key player in the sterol regulatory element-binding protein (SREBP) pathway that controls the cellular homeostasis of sterol . It consists of a luminal domain, eight transmembrane segments from which TM2-TM6 corresponds to the SSD (

) and a WD40 domain at the C-terminal .
PARP14, second type I KH domain (PARP14_KH_2)
Type: Domain

This domain is found in human Protein mono-ADP-ribosyltransferase PARP14 and related proteins. It is a KH domain found second in human PARP14.

PARP14 is a large multidomain protein which in the N-terminal half contains a series of consecutive RRM and KH domains that are known to be nucleic acid-binding. PARP14 is involved in multiple signaling pathways linked to cancer, inflammation, and infection. PARP14 is an ADP-ribosyltransferase that mediates mono-ADP-ribosylation of glutamate residues on target proteins . In contrast to PARP1 and PARP2, it is not able to mediate poly-ADP-ribosylation .
PARP14, first type I KH domain (PARP14_KH_1)
Type: Domain

This domain is found in human Protein mono-ADP- ribosyltransferase PARP14 and related proteins. It is a KH domain found first in human PARP14.

PARP14 is a large multidomain protein which in the N-terminal half contains a series of consecutive RRM and KH domains that are known to be nucleic acid-binding. PARP14 is involved in multiple signaling pathways linked to cancer, inflammation, and infection. PARP14 is an ADP-ribosyltransferase that mediates mono-ADP-ribosylation of glutamate residues on target proteins . In contrast to PARP1 and PARP2, it is not able to mediate poly-ADP-ribosylation .
PARP14, third type I KH domain (PARP14_KH_3)
Type: Domain

This domain is found in human Protein mono-ADP- ribosyltransferase PARP14 and related proteins. It is a KH domain found third in PARP14.

PARP14 is a large multidomain protein which in the N-terminal half contains a series of consecutive RRM and KH domains that are known to be nucleic acid-binding. PARP14 is involved in multiple signaling pathways linked to cancer, inflammation, and infection. PARP14 is an ADP-ribosyltransferase that mediates mono-ADP-ribosylation of glutamate residues on target proteins . In contrast to PARP1 and PARP2, it is not able to mediate poly-ADP-ribosylation .
PARP14, fourth type I KH domain (PARP14_KH_4)
Type: Domain

This domain is found in human Protein mono-ADP-ribosyltransferase PARP14 and related proteins. It is a KH domain found fourth in PARP14.

PARP14 is a large multidomain protein which in the N-terminal half contains a series of consecutive RRM and KH domains that are known to be nucleic acid-binding. PARP14 is involved in multiple signaling pathways linked to cancer, inflammation, and infection. PARP14 is an ADP-ribosyltransferase that mediates mono-ADP-ribosylation of glutamate residues on target proteins . In contrast to PARP1 and PARP2, it is not able to mediate poly-ADP-ribosylation .
PARP14, fifth type I KH domain (PARP14_KH_5)
Type: Domain

This domain is found in human Protein mono-ADP-ribosyltransferase PARP14 and related proteins. It is a KH domain found fifth in PARP14.

PARP14 is a large multidomain protein which in the N-terminal half contains a series of consecutive RRM and KH domains that are known to be nucleic acid-binding. PARP14 is involved in multiple signaling pathways linked to cancer, inflammation, and infection. PARP14 is an ADP-ribosyltransferase that mediates mono-ADP-ribosylation of glutamate residues on target proteins . In contrast to PARP1 and PARP2, it is not able to mediate poly-ADP-ribosylation .
PARP14, sixth type I KH domain (PARP14_KH_6)
Type: Domain

This domain is found in human Protein mono-ADP-ribosyltransferase PARP14 and related proteins. It is a KH domain found sixth in PARP14.

PARP14 is a large multidomain protein which in the N-terminal half contains a series of consecutive RRM and KH domains that are known to be nucleic acid-binding. PARP14 is involved in multiple signaling pathways linked to cancer, inflammation, and infection. PARP14 is an ADP-ribosyltransferase that mediates mono-ADP-ribosylation of glutamate residues on target proteins . In contrast to PARP1 and PARP2, it is not able to mediate poly-ADP-ribosylation .
PARP14-like, eighth type I KH domain (PARP14_KH_8)
Type: Domain

This domain is found in human Protein mono-ADP-ribosyltransferase PARP14 and related proteins including mono-ADP-ribosyltransferase PARP9. It is a KH domain found eighth in PARP14.

PARP14 is a large multidomain protein which in the N-terminal half contains a series of consecutive RRM and KH domains that are known to be nucleic acid-binding. PARP14 is involved in multiple signaling pathways linked to cancer, inflammation, and infection. PARP14 is an ADP-ribosyltransferase that mediates mono-ADP-ribosylation of glutamate residues on target proteins . In contrast to PARP1 and PARP2, it is not able to mediate poly-ADP-ribosylation .

PARP9 in association with E3 ligase DTX3L, plays a role in DNA damage repair and in immune responses including interferon-mediated antiviral defenses . It suppresses PARP14-mediated STAT6 ADP-ribosylation . During DNA repair, PARP1 recruits PARP9/BAL1-DTX3L complex to DNA damage sites via PARP9 binding to ribosylated PARP1 . PARP9 is a multidomain protein, predicted to contain only a single KH domain.
PARP14, second RRM domain (RRM_PARP14_2)
Type: Domain

This domain is found in human Protein mono-ADP- ribosyltransferase PARP14 and related proteins. It is an RRM domain found second in PARP14.

PARP14 is a large multidomain protein which in the N-terminal half contains a series of consecutive RRM and KH domains that are known to be nucleic acid-binding. PARP14 is involved in multiple signaling pathways linked to cancer, inflammation, and infection. PARP14 is an ADP-ribosyltransferase that mediates mono-ADP-ribosylation of glutamate residues on target proteins . In contrast to PARP1 and PARP2, it is not able to mediate poly-ADP-ribosylation .
PAR14-like, first RRM domain (PARP14_RPM_1)
Type: Domain

This domain is found at the N-terminal of proteins homologous to human mono-ADP-ribosyltransferase PARP14. It is also present in E3 ubiquitin-protein ligase DTX3L and RRM containing proteins. It shares significant sequence similarity with NID domain found in IFP35 and Nmi. These domains are predicted to adopt similar structures with topology typical for RNA-binding domains.

PARP14 is a large multidomain protein which in the N-terminal half contains a series of consecutive RRM and KH domains that are known to be nucleic acid-binding. PARP14 is involved in multiple signaling pathways linked to cancer, inflammation, and infection. PARP14 is an ADP-ribosyltransferase that mediates mono-ADP-ribosylation of glutamate residues on target proteins . In contrast to PARP1 and PARP2, it is not able to mediate poly-ADP-ribosylation .

DTX3L is a E3 ubiquitin-protein ligase which, in association with ADP-ribosyltransferase PARP9, plays a role in DNA damage repair and in interferon- mediated antiviral responses . In response to DNA damage, DTX3L mediates monoubiquitination of 'Lys-91' of histone H4 (H4K91ub1) . In association with PARP9, this protein plays a role in antiviral responses by mediating 'Lys-48'-linked ubiquitination of encephalomyocarditis virus (EMCV) and human rhinovirus (HRV) C3 proteases and promotes their proteasomal-mediated degradation .
ZMYND11/ZMYD8, MYND zinc finger (MYND_ZMYND11_ZMYD8)
Type: Domain

This entry represents the MYND zinc finger from ZMYND11 and ZMYND8 from human and related sequences. These are chromatin readers that recognise methylated histones; ZMYND11 recognises H3.3 trimethylated at 'Lys-36' (H3.3K36me3) and regulates RNA polymerase II elongation. ZMYND8 recognises histone H3.1 dimethylated at 'Lys-36' and histone H4 acetylated at 'Lys-16' and histone H3 methylated at 'Lys-4' and histone H4 acetylated at 'Lys-14' .
ZMYND11, coiled-coil (ZMYND11_CC)
Type: Domain

This entry represents a coiled-coil domain that self associates to form a dimeric arrangement found in animal ZMYND11 proteins. This domain is adjacent to a MYND zinc finger .

The Zinc finger MYND domain-containing protein 11 family functions as a chromatin reader, specifically recognising and binding to histone H3.3 trimethylated at Lys-36 (H3.3K36me3). It plays a role in regulating RNA polymerase II elongation, acting as a transcription corepressor by modulating the polymerase during the elongation stage. The family's PWWP domain adopts a five-stranded β-barrel fold and binds to H3.3K36me3 via a conserved aromatic cage. This group of proteins is involved in the specific recognition of H3.3 histone by encapsulating the Ser 31 residue of H3.3 in a composite pocket formed by tandem bromo-PWWP domains. Additionally, members have a role in tumour suppression by repressing transcriptional programs essential for tumour cell growth and can bind non-specifically to dsDNA. In the context of microbial infection, it can inhibit viral-mediated transcriptional activation and host cell proliferation .
PRTase associated wHTH domain (wHTH-PRTase_assoc)
Type: Domain

This entry represents a wHTH domain found at the C-terminal of proteins containing PRTase-CE (

) domain in the retron antiviral immunity system and in similar uncharacterised prokaryotic sequences.
OLD-like TOPRIM domain (OLD-like_TOPRIM_dom)
Type: Domain

This entry represents a Toprim domain predicted to act as a nuclease like those seen in the OLD systems . It is found associated with
Nesprin-1, spectrin repeats region (Spectrin_SYNE1)
Type: Domain

This entry represents a region of spectrin repeats found in human Nesprin-1/2 (SYNE1/2) and its animal homologues, including Muscle-specific protein 300 kDa from Drosophila melanogaster (Msp300).

SYNE1 is a a multi-isomeric modular protein which forms a linking network between organelles and the actin cytoskeleton to maintain the subcellular spatial organisation. This protein has been associated with several severe disorders. SYNE1 and SYNE2 mediate centrosome migration and are both essential for ciliogenesis . SYNE2 assemble with SUN2 in arrays of transmembrane actin-associated nuclear (TAN) lines which are bound to F-actin cables and couple the nucleus to retrograde actin flow during actin-dependent nuclear movement .

Msp300 collaborates with Klar to promote even spacing of the myonuclei at the periphery of striated muscle fibres by mediating a tight association between its nuclear ring structure and the plus ends of a unique astral MT network. It is essential for anchoring nuclei, mitochondria and endoplasmic reticulum structures to the Z-disks . In fat body cells, it anchors at the cytoplasmic surface of the nucleus part of the perinuclear non-centrosomal microtubule-organizing centres which function to accommodate the organisation of microtubule networks to control nuclear positioning and dynein motor-based retrograde endosomal trafficking .
LTI65/LTI78, NYQTKV repeat (LTI65_LTI78_NYQTKV)
Type: Domain

This entry represents a disordered region found in LTI78 and LTI65 from Arabidopsis and related plant proteins. This region consists of repeats containing the conserved sequence NYQTKV. It is found N-terminal of the CAP160 repeat (

).

LTI78 and LTI65 are involved in responses to abiotic stress .
LTI65/LTI78, PGEED repeat (LTI65/LTI78_PGEED)
Type: Domain

This entry represents a disordered region found in LTI78/LTI65 from Arabidopsis thaliana and related plant proteins. This region consists of repeats containing the conserved PGEED sequence and is located C-terminal of the CAP160 repeat (

).

LTI78 and LTI65 are involved in responses to abiotic stress .
MBTPS1, third domain (MBTPS1_3rd)
Type: Domain

This domain is found in the family of serine proteases such as MBTPS1 and SBT6.1 that are involved in regulated intramembrane proteolysis (RIP) of various substrates, playing a crucial role in cellular signalling and regulation. This domain is predicted to fold into a globular structure with an Ig-like fold.

MBTPS1 proteases cleave after hydrophobic or small residues, with a preference for Arg or Lys at the P4 position . They are responsible for the proteolytic activation of sterol regulatory element-binding proteins (SREBPs), cyclic AMP-dependent transcription factors (ATF6 and ATF6B), and other factors like BDNF, GNPTAB, and FAM20C . In plants, SBT6.1 participate in stress response signalling and cell wall remodelling by processing factors like BZIP17 and pectinesterases .
PLCG, EF-hand domain 2 (PLCG_EF-hand_2)
Type: Domain

This entry represents an EF-hand like domain found in animal 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma proteins (PLCG). PLCG1 plays a role in actin reorganisation and cell migration . PLGC1 has a critical role in maintaining immune homeostasis . PLCG2 is a crucial enzyme in transmembrane signalling. This protein has been associated with several disorders . PLCG structure comprises several key domains: an N-terminal PH domain, EF-hand motifs, catalytic X and Y domains forming a TIM-barrel, a C2 domain, a split PH domain, two SH2 domains (N-terminal and C-terminal), and an SH3 domain .

This domain is also found in the orthologue from C.elegans 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma plc-3, which regulates basal and ovulatory sheath cell contractions .
Immunity protein TriTu (TriTu)
Type: Family

This entry represents the immunity protein TriTu from Salmonella enterica and related batcerial proteins. TriTu is a part of the TreTu/TriTu toxin/antitoxin system. TriTu immunity protein neutralises TreTu activity by acting like a lid that closes the TreTu catalytic site and traps the NAD+ . TriTu is composed of a flat five-stranded antiparallel β-sheet flanked on one side by two α-helices (

) .