SII-SWORD/CoKE huggingface dataset:
SAC3 helical domain (SAC3_helical)
Type: Domain

This domain is found in fungal proteins, including the nuclear mRNA export protein SAC3. It has been suggested this domain provides a scaffold within the yeast Sac3:Cdc31:Sus1:Thp1 (TREX-2) complex to integrate interactions between protein complexes to facilitate the coupling of transcription and mRNA export during gene expression .
Protein of unknown function DUF3810 (DUF3810)
Type: Family

This family of bacterial proteins is functionally uncharacterised. Proteins in this family are typically between 333 and 377 amino acids in length and contain a conserved HEXXH sequence motif that is characteristic of metallopeptidases. This family may therefore belong to an as yet uncharacterised family of peptidase enzymes.
Protein of unknown function DUF2705 (DUF2705)
Type: Family

This bacterial family of proteins has no known function.
Protein of unknown function DUF2710 (DUF2710)
Type: Family

This family of uncharacterised proteins appears to be restricted to Mycobacteriaceae.
Inorganic phosphate transporter chaperone Pho86 (Pho86)
Type: Family

Pho86p is an ER chaperone required for chaperoning multi-pass membrane proteins through the ER membrane compartment . It is essential for growth when phosphate levels are limiting , being involved in the regulation of Pho84p, a high-affinity phosphate transporter, which is localised to the endoplasmic reticulum (ER) in low phosphate medium. When the level of phosphate increases Pho84p is transported to the vacuole. Pho86p is required for packaging of Pho84p in to COPII vesicles .
Sec16, Sec23-binding domain (Sec16_Sec23-bd)
Type: Domain

COPII coat assembly protein sec16 (Sec16) is a multi-domain vesicle coat protein that binds to COPII-coated vesicles, regulating the transport of secretory proteins from the endoplasmic reticulum. This entry represents the C-terminal domain of Sec16 from eukaryotes and related sequences such as Protein transport protein Sec16A-B and Sec31A-B. This domain adopts a TPR-like fold and has been shown to act as a protein-protein interaction platform that binds Sec23 . This interaction is regulated by alternative splicing upon T-cell activation to control protein secretion . Sec16 has also been shown to respond to nutrient signalling, coupling environmental stimuli to secretory capacity .

Sec31 is a component of the COPII coat complex that mediates formation of transport vesicles from the ER. The central α-helical unit of Sec31 is structurally similar to four large architectural nucleoporins. This α-helical unit, common to COPII and nuclear pore complex proteins, has been termed the ancestral coatomer element 1 (ACE1) .
NigD-like N-terminal OB domain (NigD-like_OB_dom)
Type: Domain

This entry represents the N-terminal OB domain found in a group of proteins from bacteroidetes, including NigD1 (BT_4005) from Bacteroides thetaiotaomicron and the predicted mannosylglucose phosphorylase BF0700 from Bacteroides fragilis (

) .

NigD1 is a protein encoded adjacent to genes required for biosynthesis and regulation of lipopolysaccharides (LPS) and phospholipids. This protein was shown to be involved in controlling outer membrane vesicles (OMV) production and act as a molecular switch for OMV biogenesis . NigD1 controls, via currently unknown mechanisms, the amount of LPS, proteins, and lipids allocated to OMVs .
SipL, SPOCS domain (SipL_SPOCS_dom)
Type: Domain

This entry represents the SPOCS domain found in three copies in SipL from Clostridium difficile, N-terminal to the LysM domain (

) . SipL (for SpoIVA-interacting protein) is involved in coat localization and, together with SpoIVA, is a critical spore morphogenetic protein .
Putative amidase domain (Amidase_6)
Type: Domain

This entry represents a putative amidase domain.
SusD-like (SusD-like)
Type: Family

Mammalian distal gut bacteria have an expanded capacity to utilise glycans. In the absence of dietary sources, some species rely on host-derived mucosal glycans. The ability of Bacteroides thetaiotaomicron, a prominent human gut symbiont, to forage host glycans contributes to both its ability to persist within an individual host and its ability to be transmitted naturally to new hosts at birth.

This entry represents a family of SusD-like proteins, one member of which, BT1043 (

), is an outer membrane lipoprotein from B. thetaiotaomicron that is involved in host glycan metabolism . The structures of this and other SusD-homologues in the family are dominated by tetratrico peptide repeats that may facilitate association with outer membrane β-barrel transporters required for glycan uptake. The structure of BT1043 complexed with N-acetyllactosamine reveals that recognition is mediated via hydrogen bonding interactions with the reducing end of beta-N-acetylglucosamine, suggesting a role in binding glycans liberated from the mucin polypeptide.
Natural killer cell receptor 2B4, immunoglobulin domain (NK_rcpt_2B4_Ig_dom)
Type: Domain

2B4 is a transmembrane receptor which is expressed primarily on natural killer (NK) cells. It plays a role in activating NK-mediated cytotoxicity through its interaction with CD48 on target cells in a subset of CD8 T cells . The structure of 2B4 consists of an immunoglobulin variable domain fold and contains two β-sheets. One of the β-sheets, the six-stranded sheet, contains structural features that may have a role in ligand recognition and receptor function .

This entry represents the 2B4 immunoglobulin domain.
Single-stranded DNA binding protein DdrB-like (ssDNA-bd_DdrB-like)
Type: Family

This family includes the Deinococcus DdrB protein, a ssDNA binding protein induced by ionizing radiation which has a role in genome reconstitution . The structure of DdrB is known . This family also includes some possibly distantly related cyanobacterial proteins.
YmaF (YmaF)
Type: Family

This family of proteins contain 6 HXH motifs and is named after the B. subtilis YmaF protein. The function of these proteins is unknown but it seems likely that they are involved in metal binding.
Nuclear Testis protein, N-terminal (NUT_N)
Type: Domain

This domain is found in the N-terminal region of Nuclear Testis (NUT) proteins. The NUT gene is found fused to BRD3 or BRD4 genes in some aggressive types of carcinoma, due to chromosomal translocations . The BRD family proteins contain two bromodomains that bind transcriptionally active chromatin through associations with acetylated histones H3 and H4 . BRD proteins are crucial for the regulation of cell cycle progression.
NUT family (NUT)
Type: Family

The gene encoding Nuclear Testis (NUT) protein is found fused to BRD3 or BRD4 genes in some aggressive types of carcinoma due to chromosomal translocations . Proteins of the BRD family contain two bromodomains that bind transcriptionally active chromatin through associations with acetylated histones H3 and H4 . Such proteins are crucial for the regulation of cell cycle progression. On the other hand, little is known about NUT protein function.
Lipocalin-like domain (Lipocalin-like)
Type: Domain

The lipocalin fold is dominated by eight β-strands which together form a cup-shaped antiparallel β-barrel that encloses an internal ligand-binding site . This entry represents domains with a fold that is related to the to the lipocalin fold.
TACC protein, fungi (TACC_fungi)
Type: Family

TACC proteins are present in different organisms, ranging from yeasts to mammals. Schizosaccharomyces pombe has one TACC protein, known as Alp7 or Mia1p . Alp7/TACC consists of two domains: the N-terminal half that contains the nuclear localization signal (NLS) and has no homology to the other TACC members, and the C-terminal half, which consists of the conserved coiled-coil TACC domain . Alp7/TACC forms a complex with Alp14/TOG and localizes to microtubules, SPBs and kinetochores . This complex is necessary for mitotic and meiotic spindle assembly and proper chromosome segregation .

The homologue from S. cerevisiae, Slk19, also has a role in spindle assembly and stability, and it is required for proper chromosome segregation .
Suppressor of fused C-terminal (SUFU_C)
Type: Domain

This entry represents the C-terminal domain of eukaryotic suppressor of fused (Sufu) proteins. It folds into a domain that comprises a four-stranded and a six-stranded β-sheet, both with mixed topologies, which are connected by two antiparallel α-helices .

Sufu is a repressor of the Gli and Ci transcription factors of the Hedgehog signalling cascade . It functions by binding to these proteins and preventing their translocation to the nucleus. The Sufu C-terminal domain binds to the N-terminal of Gli/Ci, while the N-terminal of Sufu binds to the C-terminal of Gli/Ci. This dual binding mechanism is likely to be an evolutionary advancement in this signalling cascade, which is not present in bacterial homologues .
Domain of unknown function DUF3805 (DUF3805)
Type: Domain

This entry represents an N-terminal domain found in a family of bacterial proteins, whose function is unknown. In two related Bacteroides species, the gene for members of this family lies immediately upstream from a putative ATP binding component of an ATP transporter and a putative histidinol phosphatase.

The structure of this domain is strikingly similar to the N-terminal structure of 1tui, also of unknown function. The domain carries four conserved tryptophan residues.
Nuclear pore assembly and biogenesis protein, APQ12 (APQ12)
Type: Family

This is a family of conserved fungal proteins involved in nuclear pore assembly . APQ12 is an integral membrane protein of the nuclear envelope (NE) and endoplasmic reticulum. Its absence leads to a partial block in mRNA export and cold-sensitive defects in the growth and localisation of a subset of nucleoporins, particularly those asymmetrically localised to the cytoplasmic fibrils . The defects in nuclear pore assembly appear to be due to defects in regulating membrane fluidity .
Dynein heavy chain, AAA module D4 (Dynein_heavy_chain_D4_dom)
Type: Domain

The 380kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases. The core of the 380kDa motor unit contains a concatenated chain of six AAA modules, of which four (D1 - D4) correspond to the ATP binding sites with P-loop signatures described previously, and two (D5, D6) are modules in which the P loop has been lost in evolution. This particular entry represents the D4 ATP-binding domain of the motor .
Negative regulator of Ofd1/Enhancer of translation termination 1 (Nro1/ETT1)
Type: Family

In fission yeast, Nro1 is a positive regulator of the stability of Sre1N, the sterol regulatory element-binding protein, which is an ER membrane-bound transcription factor that controls adaptation to low oxygen-growth . In addition, the fission yeast Nro1 is a direct inhibitor of a protein that inhibits SreN1 degradation, Ofd1 (an oxoglutamate deoxygenase). The outcome of this reactivity is that Ofd1 acts as an oxygen sensor that regulates the binding of Nro1 to Ofd1 to control the stability of Sre1N .

This entry also represents ETT1, an Nro1 ortholog . ETT1 is required for correct translation termination and probably involved in regulation of hypoxic gene expression in association TPA1 . It inhibits replication of Brome mosaic virus .
ATPase expression protein 2, mitochondrial (ATPase_expression_mit)
Type: Family

ATPase expression protein 2 (also known as ATP13 in some species) is necessary for the expression of subunit 9 of mitochondrial ATPase. The protein has a basic amino terminal signal sequence that is cleaved upon import into mitochondria .
Phosphatidylglycerol lysyltransferase, C-terminal (LPG_synthase_C)
Type: Domain

This domain can be found in the C-terminal region of phosphatidylglycerol lysyltransferase mprF, which catalyses the transfer of a lysyl group from L-lysyl-tRNA(Lys) to membrane-bound phosphatidylglycerol (PG), which produces lysylphosphatidylglycerol (LPG) . This is the hydrophilic domain which includes the active site . It is also be found in lysylphosphatidylglycerol biosynthesis bifunctional protein LysX, which is the two-domain lysyl-transferase (mprF)-lysyl-tRNA synthetase (lysU) protein is responsible for LPG production and in LysX2 .
Protease inhibitor, falstatin (Prot_Inh_falstatin)
Type: Family

This family of peptidase inhibitors is expressed in plasmodial protozoal species. Falstatin is found to be a potent reversible inhibitor of the P. falciparum cysteine proteases falcipain-2 and falcipain-3, as well as other parasite- and non-parasite-derived cysteine proteases, but is only a relatively weak inhibitor of the P. falciparum cysteine proteases falcipain-1 and dipeptidyl aminopeptidase 1. Thus, P. falciparum requires expression of falstatin to limit proteolysis by certain host or parasite cysteine proteases during erythrocyte invasion . In addition, in the mosquito vector, it is essential for the gliding motility of hemocoel sporozoites and, therefore, for salivary gland invasion and the subsequent transmission from the mosquito to the mammalian host .
Protein of unknown function DUF2682 (DUF2682)
Type: Family

The function of these viral proteins is not known.
Condensin complex subunit 1, N-terminal (Condensin_cplx_su1_N)
Type: Domain

Condensin is a multi-subunit protein complex that acts as an essential regulator of chromosome condensation . It contains both SMC (structural maintenance of chromosomes) and non-SMC subunits. Condensin plays an important role during mitosis in the compaction and resolution of chromosomes to remove and prevent catenations that would otherwise inhibit segregation. This is thought to be achieved by the introduction of positive supercoils into relaxed DNA in the presence of type I topoisomerases and converts nicked DNA into positive knotted forms in the presence of type II topoisomerases. During interphase condensin promotes clustering of dispersed loci into subnuclear domains and inhibits associations between homologues. In meiosis, condensin has been shown to influence the number of crossover events by regulating programmed double-strand breaks. Roles in gene regulation and lymphocyte development have also been defined.

Condensin subunit 1 (known as Cnd1 in Schizosaccharomyces pombe (Fission yeast), and XCAP-D2 in Xenopus laevis laevis) represents one of the non-SMC subunits in the complex. This subunit is phosphorylated at several sites by Cdc2. This phosphorylation process increases the supercoiling activity of condensin .

This entry represents the conserved N-terminal domain of Cnd1.
Domain of unknown function DUF3835 (DUF3835)
Type: Domain

This domain is found in a number of fungal proteins whose function is unknown.
Ribosomal RNA-processing protein 7, C-terminal domain (RRP7_C)
Type: Domain

Ribosomal RNA-processing protein 7 (RRP7) is an essential protein in yeast that is involved in pre-rRNA processing and ribosome assembly . It is speculated to be required for correct assembly of rpS27 into the pre-ribosomal particle .

This entry represents the C-terminal domain of RRP7.
Protein of unknown function DUF3845 (DUF3845)
Type: Family

This entry represents a family of uncharacterised bacterial proteins. One member,

, shows significant structural similarity to TNF-like jelly roll fold, which may indicate an immunomodulatory function or a bioadhesion role .
Protein of unknown function DUF3852 (DUF3852)
Type: Family

This entry represents a family of uncharacterised bacterial proteins found by clustering human gut metagenomic sequences .
Domain of unknown function DUF3859 (DUF3859)
Type: Domain

This entry represents a functionally uncharacterised domain, which is found in bacterial proteins.
MOZART2 family (MOZART2)
Type: Family

The MOZART2 family of proteins (also known as FAM128 and Mitotic-spindle organizing protein 2) operate as part of the gamma-tubulin ring complex, gamma-TuRC, one of the complexes necessary for chromosome segregation. This complex is located at centrosomes and mediates the formation of bipolar spindles in mitosis; it consists of six subunits. However, unlike the other four known subunits, the MOZART proteins, both 1 and 2, do not carry the conserved 'Spc97-Spc98' GCP domain, so the TUBGCP nomenclature cannot be used for it. The exact function of MOZART2 is not clear .
Mating-type protein A-alpha/beta 1, N-terminal (Mating-type_A-alpha/beta_1_N)
Type: Domain

This domain is found in some fungi and is the N-terminal of a homeodomain-containing transcription factor protein involved in mating .
Domain of unknown function DUF3863 (DUF3863)
Type: Domain

This entry represents a functionally uncharacterised domain found in bacterial sequences. The structure of one of the sequences,

from Parabacteroides distasonis atcc 8503, has been determined.
Domain of unknown function DUF3864 (DUF3864)
Type: Domain

This entry represents a functionally uncharacterised domain found in bacterial sequences. The structure of one of the sequences,

from Parabacteroides distasonis atcc 8503, has been determined.
tRNA-splicing endonuclease, subunit Sen54, N-terminal (tRNA_splic_suSen54_N)
Type: Domain

tRNA-splicing endonucleases (

) catalyse the endonucleolytic cleavage of pre tRNA at the 5' and 3' splice sites to release the intron and produces two half tRNA molecules bearing 5' hydroxyl and 2', 3'-cyclic phosphate termini . The genes encoding these proteins are homologous in eukaryotes and archea. The eukaryotic tRNA-splicing endonucleases are heterotetrameric while the archaeal endonucleases can be split into homodimeric and homotetrameric subgroups.

This entry represents the N-terminal domain of Sen54, a non-catalytic subunit of the tRNA-splicing endonuclease complex. Defects in human Sen54 are a cause of pontocerebellar hypoplasia type 4 .
tRNA-splicing endonuclease, subunit Sen54 (tRNA_splic_suSen54)
Type: Family

tRNA-splicing endonucleases (

) catalyse the endonucleolytic cleavage of pre tRNA at the 5' and 3' splice sites to release the intron and produces two half tRNA molecules bearing 5' hydroxyl and 2', 3'-cyclic phosphate termini . The genes encoding these proteins are homologous in eukaryotes and archea. The eukaryotic tRNA-splicing endonucleases are heterotetrameric while the archaeal endonucleases can be split into homodimeric and homotetrameric subgroups.

Sen54 is a non-catalytic subunit of the tRNA-splicing endonuclease complex. Defects in human Sen54 are a cause of pontocerebellar hypoplasia type 4 .
Stretch-activated cation channel MID1/Yam8 (MID1/Yam8)
Type: Family

In Saccharomyces cerevisiae, Mid1 is a yeast plasma membrane protein required for Ca2+ influx induced by the mating pheromone alpha-factor during the mating process . The protein is composed of 548-amino-acid residues, contains four hydrophobic regions (H1, H2, H3 and H4) and two cysteine-rich regions (C1 and C2) at the C terminus. H1 appears to be a signal sequence necessary for the alpha-factor-induced delivery to the plasma membrane. The region from H1 to H3 is required for the localisation of Mid1 in the plasma and ER membranes. C1 and C2 are thought to be involved in oligomerisation via the formation of disulphide bonds. Trafficking of Mid1-GFP to the plasma membrane is dependent on the N-glycosylation of Mid1 and the transporter protein Sec12. This suggests that the trafficking of Mid1-GFP to the plasma membrane requires a Sec12-dependent pathway from the ER to the Golgi, and that Mid1 is recruited via a Sec6- and Sec7-independent pathway from the Golgi to the plasma membrane.

This entry also includes Yam8/Ehs1 from Schizosaccharomyces pombe. Ehs1 is required for Ca2+ influx and for vitality of cells in a late, pheromone-induced event of the mating process requiring calcium-induced signalling .
Protein of unknown function DUF3836 (DUF3836)
Type: Family

This entry represents a family of bacterial proteins of unknown function. These proteins fold into a single-layer anti-parallel β-sheet, comprised of three or four twisted β-hairpin repeats. Small clusters of hydrophobic residues adjacent to the turns are likely to play a significant role in the structural stability of these domains and compensate for the lack of a compact hydrophobic core .
Sec16, central conserved domain (Sec16_CCD)
Type: Domain

The yeast protein Sec16 plays a key role in the formation of coat protein II vesicles, which mediate protein transport from the endoplasmic reticulum (ER) to the Golgi apparatus . Mammals have two isoforms of this protein - Sec16A and Sec16B. Sec16A appears to be the primary orthologue as it has the highest sequence similarity to the yeast sequence. Sec16B is involved in export of the peroxisomal membrane biogenesis factor peroxin 16 .

This entry represents the central conserved domain (CCD) of Sec16, found in all isoforms of this protein. The CCD is necessary for targeting of the protein to the ER .
Protein of unknown function DUF2631 (DUF2631)
Type: Family

This entry represents a family of proteins from Actinobacteria, including MSMEG_2575 from Mycolicibacterium smegmatis (

) .
Bacteriophage baseplate structural protein Gp28 (Phage_T4_Gp28)
Type: Family

Gp28 is a structural component of the central part of the bacteriophage T4 baseplate. The membrane-bound protein forms a complex with an another baseplate structural component, Gp27 . This complex may function as an initiator of the central hub assembly.
Capsid protein VP4, dicistrovirus (VP4_dicistrovir)
Type: Domain

This domain represents VP4, a minor capsid protein from dicistroviridae which is processed from the capsid polyprotein. The dicistroviridae is a group of small, RNA-containing viruses that are closely structurally related to the picornaviridae. VP4 is a short, extended polypeptide chain found within the viral capsid, at the interface between the external protein shell and packaged RNA genome .
Mycothiol-dependent maleylpyruvate isomerase, metal-binding domain (MDMPI_metal-binding)
Type: Domain

This entry represents the N-terminal metal-binding domain in mycothiol-dependent maleylpyruvate isomerases .
DNA maturase, bacteriophage T7-like (DNA_matur_Phage_T7-like)
Type: Family

This entry represents Gp18 (gene 18 product, also known as DNA maturase A and Terminase, small subunit gp18) from T7-like bacteriophages. In Bacteriophage T3, this protein is required for DNA packaging and functions in a complex with Gp19 .
Tegument protein, herpes virus, N-terminal domain (Tegument_herpes_virus_N)
Type: Domain

This entry represents the N-terminal domain of tegument proteins from double-stranded DNA herpesvirus.
GB virus, envelope protein (GB_virus_envelope)
Type: Domain

This domain represents an envelope protein found in polyproteins from the ssRNA GB virus, mainly genotype C.
Peptidase C62, gill-associated virus (Pept_C62_gill-assoc_virus)
Type: Family

This protease is found in polyproteins from the positive-stranded RNA virus of prawns called yellow head virus or gill-associated virus (GAV). The GAV cysteine proteinase (3C-like proteinase) is predicted to be the key enzyme in the processing of the GAV replicase polyprotein precursors, polyprotein 1a and polyprotein 1ab. This protease employs a Cys(2968)-His(2879) catalytic dyad . It is classified as family C62 in the MEROPS database.
Human herpesvirus 5 RL5A/RL6 (HHV5_RL5A/RL6)
Type: Family

This entry represents RL5A and RL6 from human herpesvirus 5. RL5A and RL6 are members of the RL11 family, which are predicted to encode membrane glycoproteins .