SII-SWORD/CoKE huggingface dataset:
WDHD1/CFT4, second beta-propeller (WDHD1/CFT4_beta-prop_2nd)
Type: Domain

This entry represents the second β-propeller domain found in the middle region of WDHD1 (also known as AND-1) from human and at the C-terminal of its orthologues from yeast, CFT4 and minichromosome loss protein 1 (Mcl1) [[28381552]]. This domain, together with the helical bundle (

) forms the SepB domain, which mediates the homotrimer formation of these proteins [[28381552]].

WDHD1 is an adaptor molecule crucial for DNA replication . It is a core replisome component that acts as a replication initiation factor. It binds directly to the CMG complex and functions as a hub to recruit additional proteins to the replication fork .

CTF4 is an accessory factor for DNA replication that plays a role in accurately duplicating the genome in vivo .
GB virus C, polyprotein N-terminal (GB_virus-C_polyprotein_N)
Type: Domain

This entry defines the N-terminal domain of the polyprotein of GB virus C; its function is not known.
Holliday junction regulator protein family C-terminal (HJURP_C)
Type: Domain

Although this family is conserved in the Holliday junction regulator, HJURP, proteins in higher eukaryotes, alongside an Scm3,

, family, its exact function is not known. The C-terminal region of Scm3 proteins has been evolving rapidly, and this short repeat at the C-terminal end can be present in up to two copies in the higher eukaryotes.
Baculoviral IAP repeat-containing protein 6 (BIRC6)
Type: Family

Baculoviral IAP repeat-containing protein 6 (BIRC6, also known as BRUCE) is an anti-apoptotic protein which can regulate cell death by controlling caspases and by acting as an E3 ubiquitin-protein ligase . It has an unusual ubiquitin conjugation system in that it could combine in a single polypeptide, ubiquitin conjugating (E2) with ubiquitin ligase (E3) activity, forming a chimeric E2/E3 ubiquitin ligase . It is crucial for normal vesicle targeting to the site of abscission, but also for the integrity of the midbody and the midbody ring, and its striking ubiquitin modification .
Domain of unknown function DUF3644 (DUF3644)
Type: Domain

This entry represents a HEPN-like domain found in bacterial proteins. The AlphaFold structures show this group of proteins is a part of the Nucleotidyltransferase substrate binding domain superfamily.
Domain of unknown function DUF3645 (DUF3645)
Type: Domain

This domain family is found in eukaryotes, and is approximately 40 amino acids in length. There is a conserved HPD sequence motif.
Paired box protein 7, C-terminal (Pax7_C)
Type: Domain

This domain is found in the C-terminal region of Pax7, which is a transcription factor playing a role in myogenesis through regulation of muscle precursor cells proliferation . Proteins containing this domain also include Pax3.
DNA polymerase III, subunit gamma/ tau, C-terminal (DNA_pol_III_gamma/tau_C)
Type: Domain

This domain is found in bacteria, and is approximately 120 amino acids in length. It is found in association with

. The proteins in this family are frequently annotated as the gamma and tau subunits of DNA polymerase III, however there is little accompanying literature to back this up.
Protein of unknown function DUF3648 (DUF3648)
Type: Family

This family of proteins is found in eukaryotes and viruses. Proteins in this family are typically between 53 and 3115 amino acids in length. There are two completely conserved residues (A and F) that may be functionally important.
Protein of unknown function DUF3649 (DUF3649)
Type: Family

This domain family is found in bacteria and eukaryotes, and is approximately 30 amino acids in length.
CASC1, C-terminal (CASC1_C)
Type: Domain

This domain can be found at the C terminus of CASC1.

The CAncer Susceptibility Candidate 1 (CASC1) gene is expressed in lung tissues, and is a strong candidate for the pulmonary adenoma susceptibility 1 (Pas1) locus, the major determinant of strain variation in lung tumour susceptibility . There appears to be a strong correlation between functional polymorphism of CASC1 and lung tumour suspectibility in mice .

Different mouse strains fall into two genotype groups (susceptible and intermediate) according to differences in the 60th codon of the CASC1 gene . The mouse CASC1 gene shares 81% similarity with the human equivalent; the role of CASC1 in human lung-cancer risk may nevertheless differ from that in mice .
Rhodanase, C-terminal (Rhodanese_C)
Type: Domain

This domain is found as the domain-extension to Rhodanase enzyme in some members of the Rhodanase family.
Transmembrane protein 131-like, N-terminal (TMEM131L_N)
Type: Domain

This domain can be found in bacterial, plant and other metazoa transmembrane proteins TMEM131L and TMEM131. Many of the members are multi-pass transmembrane proteins. This domain represents the N-terminal region .

Transmembrane protein 131-like (TMEM131L) was identified as a negative regulator of thymocyte proliferation that acts through mixed Wnt-dependent and independent mechanisms. It has two isoforms, L and S, which have different subcellular localisation. L isoform, the membrane-associated form, inhibits canonical Wnt/beta-catenin signalling through the induction of lysosome-dependent degradation of the active phosphorylated form of the LRP6 coreceptor. This protein was firstly described as containing three conserved homology domains (CHD1, 2 and 3), a transmembrane region and a C-terminal serine-rich region . Using structure prediction models from AlphaFold, it has been possible to identify the CHDs as Ig-like domains.

TMEM131 is a collagen binding transmembrane protein involved in collagen secretion by recruiting the ER-to-Golgi transport complex TRAPPIII . Human TMEM131 is predicted to contain eight Ig-like domains.
Doublesex- and mab-3-related transcription factor 1-like (DMRT1-like)
Type: Family

This family is found in eukaryotes, and is typically between 61 and 73 amino acids in length. They are suggested to be transcription factor proteins.

In Xenopus laevis, doublesex- and mab-3-related transcription factor 1a (dmrt1-a) is a transcription factor that plays a key role in male sex determination and differentiation by controlling testis development and germ cell proliferation. It acts both as a transcription repressor and activator . However, the other family member in Xenopus laevis, doublesex- and mab-3-related transcription factor DM-W (dm-w), is a transcription factor that plays a key role in female sex determination and primary ovary development. It acts as a sex-determining protein by antagonizing the transcriptional activity of male-determination protein dmrt1-a, acting as a dominant-negative type protein .
Protein of unknown function DUF3654 (DUF3654)
Type: Family

This family of proteins is found in eukaryotes. Proteins in this family are typically between 193 and 612 amino acids in length.
Adhesin P1, N-terminal (P1_N)
Type: Domain

This domain is found at the N-terminal of adhesins and hypothetical adhesin-like proteins from Mycoplasma pneumoniae and Mycoplasma genitalium, including adhesin P1 which was first identified as the major determinant for cytoadherence and gliding motility in M. pneumoniae . P1 forms a transmembrane adhesion complex with P40/P90, called 'Nap', which mediates motility and infectivity in these organisms. It consists of a large N-terminal domain that adopts a β-propeller topology and a smaller, more conserved C-terminal domain followed by a transmembrane domain. The C-terminal domain acts as a stalk connecting the large N-terminal domain with the outer surface of the cell membranes .
Severe acute respiratory syndrome coronavirus 3b protein (SARS_3b)
Type: Family

This family contains the SARS coronavirus 3b protein which is predominantly localized in the nucleolus, and induces G0/G1 arrest and apoptosis in transfected cells . SARS-CoV mRNA 3 encodes the distinct proteins ORF3a and ORF3b proteins, which are translated in different reading frames. SARS-CoV accessory protein ORF3b antagonizes interferon (IFN) function by modulating the activity of IFN regulatory factor 3 (IRF3). The IFN system functions as the first line of defense against viral infection in mammalian cells. Viral infection triggers a series of cellular events that lead to the production of IFN and several downstream antiviral genes, helping to establish an antiviral state. Viruses encode IFN antagonists to counteract the antiviral effects of IFN. SARS-CoV ORF3b, ORF6, and N proteins function as IFN antagonists. ORF3b inhibits both IFN synthesis and signaling . It localizes to the nucleus in transfected cells .
Peptidase C70, AvrRpt2 (Peptidase_C70_AvrRpt2)
Type: Family

This is a family of bacterial cysteine proteases. Papain-like cysteine proteases play a crucial role in plant-pathogen/pest interactions. On entering the host they act on non-self substrates, thereby manipulating the host to evade proteolysis . AvrRpt2 from Pseudomonas syringae pv tomato DC3000 triggers resistance to P. syringae-2-dependent defence responses, including hypersensitive cell death, by cleaving the Arabidopsis RIN4 protein which is monitored by the cognate resistance protein RPS2 .
Peptidase C71, pseudomurein endo-isopeptidase Pei (Peptidase_C71)
Type: Family

This entry represents Pseudomurein endoisopeptidase from Methanobacterium phage psiM2 (PeiP) and similar proteins from tailed bacteriophages and prokariotic phophages that belong to the group of peptidases C71. These peptidases have the catalytic triad C-H-D at the C-terminal end, a triad similar to that in thiol proteases and animal transglutaminases. PeiP catalyses the in vitro lysis of M. marburgensis cells under reducing conditions and exhibits characteristics of metal-activated peptidases .
Pestivirus nonstructural protein 2 (NS2)
Type: Family

The pestivirus NS2 peptidase is responsible for single cleavage between NS2 and NS3 of the Bovine viral diarrhea virus 1 polyprotein, a cleavage that is correlated with cytopathogenicity . The peptidase is activated by its interaction with 'J-domain protein interacting with viral protein' Jiv .
Peptidase M73, camelysin (Peptidase_M73_camelysin)
Type: Family

Camelysin is a novel surface metallopeptidase from Bacillus cereus . Camelysin prefers cleavage sites in front of aliphatic and hydrophilic amino acid residues (-OH, -SO3H, amido group), and requires zinc for activity .

This entry also includes TasA, a major biofilm matrix component from Bacillus subtilis .
Protein FAM135 (DUF3657)
Type: Family

This family is found in eukaryotes, and is approximately 60 amino acids in length. Proteins in this family contain a domain found in a group of putative lipases (

).
Domain of unknown function DUF3658 (DUF3658)
Type: Domain

This domain family is found in bacteria, and is approximately 110 amino acids in length. It is found in association with

. There are two completely conserved residues (D and R) that may be functionally important.
Protein of unknown function DUF3659 (DUF3659)
Type: Repeat

This domain family is found in bacteria and eukaryotes, and is approximately 70 amino acids in length.
U3 small nucleolar RNA-associated protein 10, N-terminal (U3snoRNP10_N)
Type: Domain

This entry represents the N-terminal domain of Utp10, which is a HEAT-repeat containing protein involved in nucleolar processing of pre-18S ribosomal RNA . Utp10 is also involved in 40S ribosome maturation . Proteins containing this domain also include HEATR1 from humans. HEATR1 is required for optimal pre-ribosomal RNA transcription by RNA polymerase I .
S-locus, receptor kinase (S-locus_recpt_kinase)
Type: Domain

This domain family is found in eukaryotes, and is approximately 40 amino acids in length. The family is found in association with

,

,

,

. There is a conserved ELPL sequence motif.
Store-operated calcium entry regulator STIMATE/YPL162C (STIMATE/YPL162C)
Type: Family

This entry includes STIMATE from animals and uncharacterised vacuolar membrane protein YPL162C from budding yeasts.
FhaA, N-terminal domain (FhaA_N)
Type: Domain

This domain can be found at the N terminus of FHA domain-containing protein Fha from Mycobacterium tuberculosis. The FHA (Fork Head Associated) domain is a phosphopeptide-specific binding domain that enables the protein to specifically bind to sequences containing phosphothreonine. FhaA is one of the major substrates of Ser/Thr protein kinases (STPK) and plays a role in the regulation of cell growth and peptidoglycan synthesis by binding to MviN. It may inhibit the late stages of peptidoglycan synthesis .
Transcriptional repressor NocA-like (Tscrpt_rep_NocA-like)
Type: Family

This domain family is found in eukaryotes, and is typically between 42 and 57 amino acids in length. There is a conserved GAY sequence motif. There is a single completely conserved residue G that may be functionally important. Nlz1 self-associated via its C terminus, interacted with Nlz2, and bound to histone deacetylases. These proteins may function as a transcriptional repressors .
Paired-box protein 2 C-terminal (Pax2_C)
Type: Domain

This domain is found in the C terminus of the paired-box protein 2, which is a transcription factor involved in embryonic development and organogenesis. It is approximately 110 amino acids in length and is found in association with

.
Protein of unknown function DUF3664, surface protein (DUF3664)
Type: Family

This family of proteins is found in eukaryotes. Proteins in this family are typically between 131 and 312 amino acids in length.
Homeobox protein (Abdominal-A)
Type: Family

This domain family is found in eukaryotes, and is approximately 30 amino acids in length. The family is found in association with

. This family is a homeobox protein involved in differentiation of embryonic cells to form the abdominal region.
Ribose-5-phosphate isomerase, C-terminal (Ribose_5_isomerase_C)
Type: Domain

This domain is found in bacteria, and is approximately 50 amino acids in length. It is found in association with

and contains two completely conserved residues (D and F) that may be functionally important.
Protein of unknown function DUF3667 (DUF3667)
Type: Family

This domain family is found in bacteria and eukaryotes, and is approximately 50 amino acids in length. There is a single completely conserved residue P that may be functionally important.
Distal-less-like homeobox protein, N-terminal domain (Distal-less_N)
Type: Domain

This domain is found in eukaryotes, and is approximately 80 amino acids in length. It is found in association with

. It is found at the N terminus of a homeobox protein involved in embryonic development and adult neural regeneration .
Domain of unknown function DUF3668 (DUF3668)
Type: Domain

This domain is found in a number of proteins, including the Cep120 protein which is associated with centriole structure and function .
Zinc finger protein, DUF3669 domain (Znf_prot_DUF3669)
Type: Domain

This domain can be found in a group of eukaryotic zinc finger proteins.
Domain of unknown function DUF3670 (DUF3670)
Type: Domain

This entry describes a domain of unknown function found in putative ATP-dependent helicase/translocase YwqA and related putative helicases. It is mainly found in bacteria. This domain is often found in association with

and

. YwqA has not been functionally characterised; it was first identified in Bacillus subtilis (strain 168) . According to structure predictions, it acquires a small β-sheet structure, surrounded by α-helices of varying lengths.
Fam-L/Fam-M-like, plasmodium (Fam-L/Fam-M-like_plasmodium)
Type: Family

This entry represents a large set of plasmodium proteins found in high copy number in subtelomeric repeats, including Fam-L and Fam-M proteins . It has been suggested that these proteins may pair to form heterodimers . Structure prediction suggests these proteins are related to RH5 and therefore may also have an adhesion role, possibly binding host receptors . This protein family was previously known as DUF3671.
Kinesin-like KIF1-type (Kinesin-like_KIF1-typ)
Type: Domain

This domain is found in kinesin-like proteins and is approximately 50 amino acids in length. It is found in some kinesin-3 family members, such as KIF1, KIF13, KIF28 and unc-104 .
Plasma membrane calcium transporting P-type ATPase, C-terminal (ATP_Ca_trans_C)
Type: Domain

This domain represents the C terminus of a calcium transporting ATPase located in the plasma membrane . This domain is found in eukaryotes, and is approximately 60 amino acids in length. It contains a conserved QTQ sequence motif.
Protein of unknown function DUF3673 (DUF3673)
Type: Family

This domain family is found in eukaryotes, and is approximately 50 amino acids in length.
Protein of unknown function DUF3675 (DUF3675)
Type: Family

This domain family is found in eukaryotes, and is approximately 120 amino acids in length. The family is found in association with

. There are two completely conserved residues (R and L) that may be functionally important.
Domain of unknown function DUF3676 (DUF3676)
Type: Domain

This domain is found in eukaryotes, and is approximately 230 amino acids in length.
Integrator complex subunit 1, RPB2-binding domain (INTS1_RPB2-bd)
Type: Domain

Integrator (INT) complex is involved in the small nuclear RNAs (snRNA) U1 and U2 transcription and in their 3'-box-dependent processing . It binds the C-terminal domain (CTD) of RNA polymerase II (Pol II) and functions as an RNA endonuclease to cleave different classes of RNAs, regulating the transcription of both protein-coding genes and noncoding elements . Integrator also associates with protein phosphatase 2A (PP2A) core enzyme to form the INTAC complex which regulates transcription through dephosphorylation of Pol II CTD. The complex consists of four modules: the backbone, the shoulder, the phosphatase and the endonuclease, formed by different integrator components.

This entry includes the Integrator complex subunit 1 (INTS1) which forms the backbone module of the complex through the association with INTS2 and INTS7 to form a rigid scaffold. The backbone and shoulder modules form a central cruciform scaffold. INTS1 is an all-α helical protein with four repetitive helix hairpin domains towards the C-terminal (R1-R4) . This entry represents a domain found towards the N-terminal region, which interacts with Pol II subunit RPB2 and form interface A .
Protein of unknown function DUF3678 (DUF3678)
Type: Family

This domain family is found in eukaryotes, and is approximately 40 amino acids in length.
Glutamine synthetase type III N-terminal (GSIII_N)
Type: Domain

This domain is found in the N terminus of glutamine synthetase type III in bacteria and eukaryotes, and is approximately 160 amino acids in length. It is found in association with

. Glutamine synthetase type III is one of the enzymes responsible for generation of glutamine through conversion glutamate to glutamine by the incorporation of ammonia (NH3) .
CopG antitoxin (CopG_antitoxin)
Type: Family

CopG antitoxin is a member of a type II toxin-antitoxin system family found in bacteria and archaea. Most antitoxins encoded by the relBE and parDE loci belong to the MetJ/Arc/CopG family of dimeric proteins which bind DNA through N-terminal ribbon-helix-helix (RHH) motifs .
Protein of unknown function DUF3681 (DUF3681)
Type: Family

This family of proteins is found in eukaryotes. Proteins in this family are typically between 112 and 212 amino acids in length. There is a single completely conserved residue G that may be functionally important.
AKNA domain (AKNA_dom)
Type: Domain

This domain can be found in microtubule organization protein AKNA (also known as AT-hook-containing transcription factor) in eukaryotes, and is approximately 110 amino acids in length. AKNA which regulates the expression of the costimulatory molecules on lymphocytes and lays a key role in cell delamination by regulating the microtubule organization .

This domain can also be found in AKNAD1 (AKNA Domain Containing 1). It has been linked to type-2 diabetes .
Sox developmental protein N-terminal (Sox_N)
Type: Domain

This domain is found in eukaryotes, and is typically between 69 and 88 amino acids in length. It is found in association with

. It contains two conserved sequence motifs: YDW and PVR. It is found in Sox8 , Sox9 and Sox10 proteins, which have structural similarity. Sox proteins are involved in developmental processes.
Protein of unknown function DUF3682 (DUF3682)
Type: Family

This domain family is found in eukaryotes, and is typically between 125 and 136 amino acids in length.
Protein of unknown function DUF3683 (DUF3683)
Type: Family

This domain family is found in bacteria, and is approximately 120 amino acids in length. The family is found in association with

,

,

.
Trafficking kinesin-binding protein, C-terminal (TRAK1/2_C)
Type: Domain

This domain can be found at the C terminus of the eukaryotic trafficking kinesin-binding proteins, including TRAK1 and TRAK2. TRAK1 binds to both kinesin-1 and dynein/dynactin, is prominently localized in axons, and is needed for normal axon outgrowth, whereas TRAK2 predominantly interacts with dynein/dynactin, is more abundantly present in dendrites, and is required for dendritic development .
Protein of unknown function DUF3684 (DUF3684)
Type: Family

This domain family is found in eukaryotes, and is typically between 1072 and 1090 amino acids in length.
Uncharacterised protein YfbK, N-terminal (Uncharacterised_YfbK_N)
Type: Domain

This domain is found in bacteria, and is approximately 100 amino acids in length. It is found in association with a von Willebrand factor type A domain (

). It contains two conserved sequence motifs: STF and DVD and two completely conserved residues (E and N) that may be functionally important. It is found in uncharacterised protein YfbK.
Dynein associated protein (Dynactin)
Type: Domain

This domain is found in eukaryotes, and is approximately 280 amino acids in length. The family is found in association with

. There is a single completely conserved residue E that may be functionally important. Dynactin has been associated with Dynein, a kinesin protein which is involved in organelle transport, mitotic spindle assembly and chromosome segregation. Dynactin anchors Dynein to specific subcellular structures .
Inositol phosphatase (Inositol_phosphatase)
Type: Domain

This domain is found in eukaryotes, and is approximately 120 amino acids in length. It is often found in association with

. It is found in hSac2, which functions as an inositol polyphosphate 5-phosphatase.
Tuftelin interacting protein, N-terminal domain (STIP/TFIP11_N)
Type: Domain

This domain is found in septin and tuftelin-interacting protein (STIP) and tuftelin-interacting protein 11 (TFIP11). STIP is essential for embryogenesis in Caenorhabditis elegans . Tuftelin-interacting protein 11 is a component of the spliceosome involved in spliceosome disassembly . TFIP11 was first identified in a yeast two-hybrid screening as a protein interacting with tuftelin, one of the presumed enamel matrix proteins .
Spiroplasma phage 1-C74, Orf1 (Phage_1-C74_Orf1)
Type: Family

This entry is represented by Spiroplasma phage 1-C74, Orf1. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.

This domain family is found in bacteria and viruses, and is typically between 79 and 104 amino acids in length. There is a conserved YRW sequence motif. There is a single completely conserved residue Y that may be functionally important.
DNA helicase IV, N-terminal domain (Helicase_IV_N)
Type: Domain

This domain is found in DNA helicase IV in bacteria. It is approximately 170 amino acids in length and is found at the N terminus of

. DNA helicase IV catalyses the unwinding of duplex DNA in the 3' to 5' direction with respect to the bound single strand in a reaction that is dependent upon the hydrolysis of ATP .
Short transient receptor potential channel 4-associated protein (TRPC4AP)
Type: Family

TRPC4AP is a substrate-specific adapter of a DCX (DDB1-CUL4-X-box) E3 ubiquitin-protein ligase complex required for cell cycle control .
GTP cyclohydrolase N-terminal (GTP_CH_N)
Type: Domain

This domain is found in bacteria and eukaryotes, and is approximately 190 amino acids in length. It is the N-terminal domain of GTP cyclohydrolase, the rate limiting enzyme in the synthesis of tetrahydrobiopterin .