SII-SWORD/CoKE huggingface dataset:
P48 protein, Baculovirus (P48_Baculovir)
Type: Family

This family comprises the Baculovirus P48 proteins. They contain two possible membrane-spanning domains and a cysteine-rich domain that are conserved in all of the proteins. The Bombyx mori (Silk moth) nuclear polyhedrosis virus protein,

, has been described as a putative DNA helicase.
Molybdopterin oxidoreductase, 4Fe-4S domain (Mopterin_OxRdtase_4Fe-4S_dom)
Type: Domain

The molybdopterin oxidoreductase 4Fe-4S domain is found in a number of reductase/dehydrogenase families, which include the periplasmic nitrate reductase precursor and the formate dehydrogenase alpha chain .

The following proteins contain this domain and belong to the molybdenium (Mo) or tungsten (W) containing enzyme family, the Mo/W bis-MGD (molybdopterin-guanine-dinucleotide) oxydoreductases :

Escherichia coli respiratory nitrate reductase (

).

Escherichia coli anaerobic dimethyl sulfoxide reductase (DMSO reductase).

Escherichia coli biotin sulfoxide reductases (genes bisC and bisZ).

Methanobacterium formicicum formate dehydrogenase (

).

Escherichia coli formate dehydrogenases -H (gene fdhF), -N (gene fdnG) and -O (gene fdoG).

Wolinella succinogenes polysulfide reductase chain.

Salmonella typhimurium thiosulfate reductase (gene phsA).

Escherichia coli trimethylamine-N-oxide reductase (

) (gene torA) .

Nitrate reductase (

) from Klebsiella pneumoniae (gene nasA), Alcaligenes eutrophus, Escherichia coli, Rhodobacter sphaeroides, Thiosphaera pantotropha (gene napA), and Synechococcus PCC 7942 (gene narB).
NUDE domain (NUDE_dom)
Type: Domain

This entry represents the conserved region of NUDE proteins. Proteins containing this domain are homologues of the nuclear distribution protein RO11 of Neurospora crassa. NUDE interacts with the NUDF via an N-terminal coiled coil domain; this is the only domain which is absolutely required for NUDE function.
Adenovirus Gp19K (Adenovirus_Gp19K)
Type: Family

The 19kDa glycoprotein (GpK19) binds the major histocompatibility (MHC) class I antigens in the endoplasmic reticulum (ER). The ER retention signal at the C terminus of Gp19K causes retention of the complex in the ER, preventing lysis of the cell by cytotoxic T-lymphocytes .
Peroxin-3 (Peroxin-3)
Type: Family

Peroxin 3 (Pex3p), also known as Peroxisomal biogenesis factor 3, has been identified and characterised as a peroxisomal membrane protein in yeasts and mammals . Two putative peroxisomal membrane-bound Pex3p homologues have also been found in Arabidopsis thaliana . They possess a membrane peroxisomal targeting signal. Pex3p is an integral membrane protein of peroxisomes, exposing its N- and C-terminal parts to the cytosol . Peroxin is involved in peroxisome biosynthesis and integrity; it assembles membrane vesicles before the matrix proteins are translocated.

In humans, defects in PEX3 are the cause of peroxisome biogenesis disorders , which include Zellweger syndrome (ZWS), neonatal adrenoleukodystrophy (NALD), infantile Refsum disease (IRD), and classical rhizomelic chondrodysplasia punctata (RCDP). These are peroxisomal disorders that are the result of proteins failing to be imported into the peroxisome.
Root UVB sensitive family (RUS_fam)
Type: Family

This family is composed of root UVB sensitive proteins and their homologues. In Arabidopsis thaliana, proteins in this family are involved in UVB-sensing and in early seedling morphogenesis and development .

In plants, these proteins play a role in auxin-transport, plant growth and development and appears to be expressed by all cells in the plant as well as in plastids. The family has been shown to play a role in vitamin B6 photo-protection and homoeostasis in plants .

In line with various literature findings describing this family in plants, it was proposed that these proteins may be directly involved in the transport of one or more forms of the vitamin B6.
Stigma-specific protein Stig1-like (Stig-like)
Type: Family

This family represents the Stig1 cysteine rich protein and related plant proteins. The tobacco stigma-specific gene, STIG1 is developmentally regulated and expressed specifically in the stigmatic secretory zone. Pistils of transgenic STIG1-barnase tobacco plants undergo normal development, but lack the stigmatic secretory zone and are female sterile. Pollen grains are unable to penetrate the surface of the ablated pistils. Application of stigmatic exudate from wild-type pistils to the ablated surface increases the efficiency of pollen tube germination and growth and restores the capacity of pollen tubes to penetrate the style . The exact function of STIG1 is unknown.

The STIG1 family is involved in various plant-specific functions, including the regulation of cell death, promotion of pollen tube growth, and modification of the interface between embryo and endosperm during seed development. Members of the family are typically cysteine-rich proteins that may undergo processing to perform their roles. For instance, a processed peptide of GRI induces cell death dependent on superoxide and salicylic acid, while STIG1 promotes pollen tube growth and binds phosphoinositol lipids, triggering an intracellular reactive oxygen species elevation. The family is also essential for the formation of structures like the embryo sheath and for the normal separation of embryo and endosperm tissues. This region contains three cystein-rich subdomains.
PT repeat (PT)
Type: Repeat

This short repeat is composed on the tetrapeptide XPTX. This repeat is found in a variety of proteins, however it is not clear if these repeats are homologous to each other.
Poxvirus M2 (Poxvirus_M2)
Type: Family

This family includes M2 protein from Vaccinia virus, also known as Early protein OPG038, and similar proteins from poxvirus. M2 plays a role in immune evasion. When secreted, inhibits T-cell activation by preventing the binding of host CD80 and CD86 to soluble CTLA4 and CD28 . In the infected cell, it may inhibit host NF kappa B activation .
Translocator protein BipB-like, C-terminal domain (BipB-like_C)
Type: Domain

This entry represents the C-terminal domain of Translocator protein BipB from Burkholderia pseudomallei and similar proteins predominantly found in proteobacteria. BipB plays a role in the bacterium-induced formation of multinucleated giant cell (MNGC), which is formed after host cell fusion, as well as in the intercellular spreading of bacteria and in the induction of apoptosis in macrophages . This domain covers most of the protein sequence in SPI-2 type 3 secretion system translocon protein SctE from Salmonella typhimurium, a component of the type III secretion system 2 (SPI-2 T3SS), also called injectisome, which is used to inject bacterial effector proteins into eukaryotic host cells (Probable). SseC/SctE2 and SseD/SctB2 are inserted into the host membrane where they form a pore and allow the translocation of effector proteins into the cytosol of target cells .
Pre-mRNA-splicing factor Cwf15/Cwc15 (Cwf_Cwc_15)
Type: Family

This family represents Cwf15/Cwc15 (from Schizosaccharomyces pombe and Saccharomyces cerevisiae respectively) and their homologues. It is a component of a complex containing Cef1 and may be involved in pre-mRNA splicing .
Protein of unknown function DUF648 (DUF648)
Type: Family

This is a family of hypothetical proteins from Chlamydia pneumoniae.
NifQ (NifQ)
Type: Family

NifQ is involved in early stages of the biosynthesis of the iron-molybdenum cofactor (FeMo-co) , which is an integral part of the active site of dinitrogenase . The conserved C-terminal cysteine residues may be involved in metal binding .
VanZ-like (VanZ-like)
Type: Domain

This entry represents a conserved sequence region found in the VanZ protein and also several phosphotransbutyrylases. VanZ confers low-level resistance to the glycopeptide antibiotic teicoplanin (Te). Analysis of cytoplasmic peptidoglycan precursors, accumulated in the presence of ramoplanin, showed that VanZ-mediated Te resistance does not involve incorporation of a substituent of D-alanine into the peptidoglycan precursors .
Yip1 domain (Yip1_dom)
Type: Domain

This entry contains proteins belonging to the Yip1 family and represents the Yip1 domain. The Yip1 integral membrane domain contains four transmembrane α-helices. The domain is characterised by the motifs DLYGP and GY. The Yip1 protein is a Golgi protein involved in vesicular transport that interacts with GTPases .
Archaeal Nre, N-terminal (Nre_N)
Type: Domain

This conserved region is found in the N-terminal region of archaeal Nre proteins. While most archaeal organisms encode only a single Nre protein, some encode two, NreA and NreB.
Archaeal Nre, C-terminal (Nre_C)
Type: Domain

This conserved region is found in the C-terminal region of archaeal Nre proteins. While most archaeal organisms encode only a single Nre protein, some encode two, NreA and NreB.
Ammonia monooxygenase/particulate methane monooxygenase, subunit C (NH3_CH4_mOase_C)
Type: Family

Ammonia monooxygenase and the particulate methane monooxygenase are both integral membrane proteins, occurring in ammonia oxidisers and methanotrophs respectively, which are thought to be evolutionarily related . These enzymes have a relatively wide substrate specificity and can catalyse the oxidation of a range of substrates including ammonia, methane, halogenated hydrocarbons and aromatic molecules . These enzymes are composed of 3 subunits -A (

), B (

) and C (

) -and contain various metal centres, including copper. Particulate methane monooxygenase from Methylococcus capsulatus str. Bath is an ABC homotrimer, which contains mononuclear and dinuclear copper metal centres, and a third metal centre containing a metal ion whose identity in vivo is not certain.

The C subunit from Methylococcus capsulatus str. Bath resides primarily in the membrane and consists of five transmembrane helices. Several conserved residues contribute to a metal binding centre .
Glutamate synthase, central-N (Glu_synth_centr_N)
Type: Domain

The central domain of glutamate synthase connects the N-terminal amidotransferase domain with the FMN-binding domain and has an α/β overall topology .

Glutamate synthase (GltS)1 is a key enzyme in the early stages of the assimilation of ammonia in bacteria, yeasts, and plants. In bacteria, L-glutamate is involved in osmoregulation, is the precursor for other amino acids, and can be the precursor for haem biosynthesis. In plants, GltS is especially essential in the reassimilation of ammonia released by photorespiration. On the basis of the amino acid sequence and the nature of the electron donor, three different classes of GltS can de defined as follows: 1) ferredoxin-dependent GltS (Fd-GltS), 2) NADPH-dependent GltS (NADPH-GltS), and 3) NADH-dependent GltS (properties of the three classes have been reviewed extensively ). The enzyme is a complex iron-sulphur flavoprotein catalysing the reductive transfer of the amido nitrogen from L-glutamine to 2-oxoglutarate to form two molecules of L-glutamate via intramolecular channelling of ammonia from the amidotransferase domain to the FMN-binding domain.

Reaction of amidotransferase domain:

L-glutamine + H2O = L-glutamate + NH3

Reactions of FMN-binding domain:

2-oxoglutarate + NH3 = 2-iminoglutarate + H2O

2e + FMNox = FMNred

2-iminoglutarate + FMNred = L-glutamate + FMNox
MbeD/MobD-like (MbeD_MobD)
Type: Family

The MbeD and MobD proteins are plasmid encoded, and are involved in the plasmid mobilisation and transfer in the presence of conjugative plasmids .
Fcf1/UTP23 (Fcf1/UTP23)
Type: Family

Utp23 share homology with PINc domain protein Fcf1. They are components of the small subunit processome (SSU) that are involved in rRNA-processing and ribosome biogenesis .
Receptor activity modifying protein (RAMP)
Type: Family

The calcitonin-receptor-like receptor can function as either a calcitonin-gene-related peptide or an adrenomedullin receptor. The receptors function is modified by receptor activity modifying protein (RAMP). RAMPs are single-transmembrane-domain proteins .
Nab1, C-terminal (Nab1_C)
Type: Domain

Nab1 and Nab2 are co-repressors that specifically interact with and repress transcription mediated by the three members of the NGFI-A (Egr-1, Krox24, zif/268) family of eukaryotic (metazoa) transcription factors . This C-terminal region is found only in the Nab1 subfamily.
Nab, N-terminal (Nab_N)
Type: Domain

Nab1 and Nab2 are co-repressors that specifically interact with and repress transcription mediated by the three members of the NGFI-A (Egr-1, Krox24, zif/268) family of eukaryotic (metazoa) transcription factors . This entry represents the N-terminal NAB domain, which interacts with the EGR1 inhibitory domain (R1) . It may also mediate multimerisation. This domain is related to the SAM domain.
NAB co-repressor, domain (NAB_co-repressor_dom)
Type: Domain

Nab1 and Nab2 are co-repressors that specifically interact with and repress transcription mediated by the three members of the NGFI-A (Egr-1, Krox24, zif/268) family of eukaryotic (metazoa) transcription factors . This entry represents a NAB domain 2 of the protein. It is necessary for transcriptional repression by the Nab proteins . It is also required for transcription activation by Nab proteins at Nab-activated promoters .
Tweety (Tweety)
Type: Family

The protein product of the Drosophila tweety (tty) gene is thought to form a trans-membrane protein with five membrane-spanning regions and a cytoplasmic C terminus. Tweety has been suggested as a candidate for a large conductance chloride channel, both in vertebrate and insect cells. Three human homologs have been identified and designated TTYH1-3. TTYH2 has been associated with the progression of cancer, and Drosophila melanogaster tweety has been assumed to play a role in development. TTYH2, and TTYH3 bind to and are ubiquinated by Nedd4-2, a HECT type E3 ubiquitin ligase, which most likely plays a role in controlling the cellular levels of tweety family proteins .
SH3-binding, glutamic acid-rich protein (Glut_rich_SH3-bd)
Type: Family

This family of proteins, which contains SH3BGRL3, is functionally uncharacterised. SH3BGRL3 is a highly conserved small protein, which is widely expressed and shows a significant similarity to glutaredoxin 1 (GRX1) of Escherichia coli which is predicted to belong to the thioredoxin superfamily. However, SH3BGRL3 lacks both conserved cysteine residues, which characterise the enzymatic active site of GRX. This structural feature raises the possibility that SH3BGRL3 and its homologues could function as endogenous modulators of GRX activity .

Adapter SH3BGRL from mammals is also included in this entry. This protein may function as a ubiquitin ligase-substrate adapter that bridges proteins together or proteins with mRNAs .
TCF25/Rqc1 (TCF25/Rqc1)
Type: Family

This entry includes ribosome quality control complex subunits TCF25 from animals and Rqc1 from budding yeasts. Rqc1 is a component of the ribosome quality control complex (RQC), a ribosome-associated complex that mediates ubiquitination and extraction of incompletely synthesized nascent chains for proteasomal degradation . TCF25 may act by increasing histone deacetylase activity at promoter regions .
ATP synthase, F0 complex, subunit J (ATP_synth_F0_jsu)
Type: Family

Transmembrane ATPases are membrane-bound enzyme complexes/ion transporters that use ATP hydrolysis to drive the transport of protons across a membrane. Some transmembrane ATPases also work in reverse, harnessing the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP.

F-ATPases (also known as ATP synthases, F1F0-ATPase, or H(+)-transporting two-sector ATPase) (

) are composed of two linked complexes: the F1 ATPase complex is the catalytic core and is composed of 5 subunits (alpha, beta, gamma, delta, epsilon), while the F0 ATPase complex is the membrane-embedded proton channel that is composed of at least 3 subunits (A-C), with additional subunits in mitochondria. Both the F1 and F0 complexes are rotary motors that are coupled back-to-back. In the F1 complex, the central gamma subunit forms the rotor inside the cylinder made of the α(3)β(3) subunits, while in the F0 complex, the ring-shaped C subunits forms the rotor. The two rotors rotate in opposite directions, but the F0 rotor is usually stronger, using the force from the proton gradient to push the F1 rotor in reverse in order to drive ATP synthesis . These ATPases can also work in reverse in bacteria, hydrolysing ATP to create a proton gradient.

This entry represents subunit J found in the F0 complex of F-ATPases from fungal mitochondria. This subunit does not appear to display sequence similarity with subunits of F-ATPases found in other organisms .
Baculovirus Y142 protein (Baculo_Y142)
Type: Family

This is a family of Baculovirus proteins including protein AC142, which is expressed in the cytoplasm and nucleus throughout infection. It is required for nucleocapsid envelopment in the budding virus to form the occlusion-derived virus and subsequent embedding of virions into polyhedra .
DltD (DltD)
Type: Family

The dlt operon (dltA to dltD) of Lactobacillus rhamnosus 7469 encodes four proteins responsible for the esterification of lipoteichoic acid (LTA) by D-alanine. These esters play an important role in controlling the net anionic charge of the poly (GroP) moiety of LTA. DltA and DltC encode the D-alanine-D-alanyl carrier protein ligase (Dcl) and D-alanyl carrier protein (Dcp), respectively. Whereas the functions of DltA and DltC are defined, the functions of DltB and DltD are unknown.
In vitro
assays showed that DltD bound Dcp for ligation with D-alanine by Dcl in the presence of ATP. In contrast, the homologue of Dcp, the Escherichia coli acyl carrier protein (ACP), involved in fatty acid biosynthesis, was not bound to DltD and thus was not ligated with D-alanine. DltD also catalyzed the hydrolysis of the mischarged D-alanyl-ACP. The hydrophobic N-terminal sequence of DltD was required for anchoring the protein in the membrane. It is hypothesized that this membrane-associated DltD facilitates the binding of Dcp and Dcl for ligation of Dcp with D-alanine and that the resulting D-alanyl-Dcp is translocated to the primary site of D-alanylation .
Phospholipase B-like (PLipase_B-like)
Type: Family

Phospholipase B (PLB) catalyses the hydrolytic cleavage of both acylester bonds of glycerophospholipids. This family of PLB enzymes has been identified in mammals, flies and nematodes but not in yeast . In Drosophila this protein was named LAMA for laminin ancestor since it is expressed in the neuronal and glial precursors that surround the lamina .
Bacterial shufflon protein, N-terminal (Shufflon_N)
Type: Domain

This domain represents the high-similarity N-terminal constant region shared by shufflon proteins. Shufflon proteins are created as a result of a clustered inversion region. The proteins retain a constant N-terminal domain, with different C-terminal domains.
Protein of unknown function DUF655 (DUF655)
Type: Family

This family includes several uncharacterised archaeal proteins.
Beet necrotic yellow vein virus, p31 (BNYVV_p31)
Type: Family

This is a family of hypothetical proteins known as p31, mostly from Beet necrotic yellow vein virus. P31, encoded by RNA4, is involved in efficient vector transmission, symptom severity and silencing suppression in roots .
XAP5 protein (XAP5)
Type: Family

These proteins are found in a wide range of eukaryotes. They are nuclear proteins, suggested to play a role in the spliceosome complex . XAP5 from Arabidopsis thaliana has been shown to be involved in light regulation of the circadian clock and photomorphogenesis .
Ninjurin (Ninjurin)
Type: Family

Ninjurin (nerve injury-induced protein) proteins are transmembrane adhesion molecules involved in nerve regeneration and in various processes such as inflammation, programmed and necrotic cell death, axonal growth, cell chemotaxis and angiogenesis .
Poxvirus A6 (Poxvirus_A6)
Type: Family

This entry represents Protein A6 from Vaccinia virus, also known as Virion morphogenesis protein OPG132, and similar proteins from poxvirus. A6 is a lipid-bound viral membrane assembly protein that plays an essential role in immature virion (IV) to mature virion (MV) transition . It functions in both crescent-shaped viral membranes formation and its enclosure to form immature virions . It also participates in targeting mature virion proteins to sites of virion assembly to ensure their correct localisation .
Shq1, C-terminal domain (Shq1_C)
Type: Domain

This entry represents a domain found C-terminal in the yeast SHQ1 protein (

) and related proteins. SHQ1 is involved in the early biogenesis steps of box H/ACA snoRNP assembly . The human homologue is required for the quantitative accumulation of H/ACA ribonucleoproteins (RNPs), including telomerase, probably through the stabilization of DKC1, from the time of its synthesis until its association with NOP10, NHP2, and NAF1 at the nascent H/ACA RNA .
Poly(A) polymerase, RNA-binding domain (PolA_pol_RNA-bd_dom)
Type: Domain

In eukaryotes, polyadenylation of pre-mRNA plays an essential role in the initiation step of protein synthesis, as well as in the export and stability of mRNAs. Poly(A) polymerase, the enzyme at the heart of the polyadenylation machinery, is a template-independent RNA polymerase that specifically incorporates ATP at the 3' end of mRNA. The crystal structure of bovine poly(A) polymerase bound to an ATP analogue at 2.5 A resolution has been determined . The structure revealed expected and unexpected similarities to other proteins. As expected, the catalytic domain of poly(A) polymerase shares substantial structural homology with other nucleotidyl transferases such as DNA polymerase beta and kanamycin transferase.
Late embryogenesis abundant protein, SMP subgroup domain (LEA_SMP_dom)
Type: Domain

LEA (late embryogenesis abundant) proteins were first identified in land plants. Plant LEA proteins have been found to accumulate to high levels during the last stage of seed formation (when a natural desiccation of the seed tissues takes place) and during periods of water deficit in vegetative organs. Later, LEA homologues have also been found in various species . They have been classified into several subgroups in Pfam and according to Bray and Dure .

This entry represents Pfam SMP, or D-34 from Dure, or group 6 from Bray.
Poly(A) polymerase, central domain (PolA_pol_cen_dom)
Type: Domain

In eukaryotes, polyadenylation of pre-mRNA plays an essential role in the initiation step of protein synthesis, as well as in the export and stability of mRNAs. Poly(A) polymerase, the enzyme at the heart of the polyadenylation machinery, is a template-independent RNA polymerase which specifically incorporates ATP at the 3' end of mRNA. The crystal structure of bovine poly(A) polymerase bound to an ATP analog at 2.5 A resolution has been determined . The structure revealed expected and unexpected similarities to other proteins. As expected, the catalytic domain of poly(A) polymerase shares substantial structural homology with other nucleotidyl transferases such as DNA polymerase beta and kanamycin transferase.
DNA polymerase processivity factor, herpesviridae (DNA_pol_proc_fac_herpes)
Type: Family

Replicative DNA polymerases are capable of polymerising tens of thousands of nucleotides without dissociating from their DNA templates. The high processivity of these polymerases is dependent upon accessory proteins that bind to the catalytic subunit of the polymerase or to the substrate. The Epstein-Barr virus (strain GD1) (HHV-4) (Human herpesvirus 4) BMRF1 protein is an essential component of the viral DNA polymerase and is absolutely required for lytic virus replication . BMRF1 is also a transactivator . This family is predicted to have a UL42-like structure .
FUN14 (FUN14)
Type: Family

This is a family of short proteins found in eukaryotes, bacteria and archaea. In humans, FUN14 domain-containing protein 1 (FUND1) acts as an activator of hypoxia-induced mitophagy, an important mechanism for mitochondrial quality control .