SII-SWORD/CoKE huggingface dataset:
Cwf19-like, C-terminal domain-1 (Cwf19-like_C_dom-1)
Type: Domain

This group of sequences contain a conserved C-terminal domain which is found in the Schizosaccharomyces pombe (Fission yeast) protein Cwf19 (

) and its homologues. Cwf19 is part of the Cdc5p complex involved in mRNA splicing . CWF19-like protein DRN1 from Saccharomyces cerevisiae (

) is involved branched RNA metabolism, modulating the turnover of lariat-intron pre-mRNAs by the lariat-debranching enzyme DBR1 (

) . This domain is found in association with

, which is generally C-terminal and adjacent to this domain. These domains contain evolutionarily conserved cysteine and histidine residues in an arrangement similar to the CCCH-class of zinc fingers .
Calcium uniporter protein, C-terminal (MCU_C)
Type: Domain

This entry represents the C-terminal domain of MCU, which is a mitochondrial inner membrane calcium uniporter that mediates calcium uptake into mitochondria . This domain can also be found in MCUb, which negatively regulates the activity of MCU .

It is also found in Chloroplastic calcium uniporter protein from Arabidopsis thaliana which mediates calcium uptake into chloroplast stroma .
Opioid growth factor receptor, disordered repeat (OGF_rcpt_rpt)
Type: Repeat

Opioid peptides act as growth factors in neural and non-neural cells and tissues, in addition to serving for neurotransmission/neuromodulation in the nervous system. The native opioid growth factor (OGF), [Met(5)]-enkephalin, is an inhibitory peptide that plays a role in cell proliferation and tissue organisation during development, cancer, cellular renewal, wound healing, and angiogenesis. OGF action is mediated by a receptor mechanism, the receptor for OGF (OGFr) is an integral membrane protein associated with the nucleus.

OGFr is distinguished by containing a series of imperfect repeats. This entry describes a proline-rich repeat found in a human opioid growth factor receptor .
Secreted thaumatin-like protein cetA-like (CetA-like)
Type: Family

This entry represents a group of proteins from ascomycetes, including Secreted thaumatin-like protein cetA from Emericella nidulans. Together with CalA, CetA plays an essential role in early conidial germination with a possible role in cell wall remodelling . The structure has been solved for a member of this family, Elicitor protein Hrip2 from Pyricularia oryzae . Blastomyces yeast phase-specific protein 1 from Ajellomyces dermatitidis (Bys1, ) also belongs to this family.
Herpesvirus BTRF1 protein (Herpes_BTRF1)
Type: Family

This is a family of Herpesvirus proteins of unknown function.
Proteasomal ubiquitin receptor Rpn13/ADRM1 (Rpn13/ADRM1)
Type: Family

This entry includes Rpn13 from budding yeasts and its homologue, ADRM1 from animals.

Rpn13 is a subunit and an ubiquitin receptor of the 19S regulatory particle of the 26S proteasome lid. The 26S proteasome is a huge macromolecular protein-degradation machine consisting of a proteolytically active 20S core, in the form of four disc-like proteins, and one or two 19S regulatory particles. The regulatory particle(s) sit on the top and or bottom of the core, de-ubiquitinate the substrate peptides, unfold them and guide them into the narrow channel through the centre of the core. Rpn13 and its homologues dock onto the regulatory particle through the N-terminal region which binds Rpn2. The C-terminal part of the domain binds de-ubiquitinating enzyme Uch37/UCHL5 and enhances its isopeptidase activity. Rpn13 binds ubiquitin via a conserved amino-terminal region called the pleckstrin-like receptor for ubiquitin, termed Pru, domain . The domain forms two contiguous anti-parallel β-sheets with a configuration similar to the pleckstrin-homology domain (PHD) fold . Rpn13's ability to bind ubiquitin and the proteasome subunit Rpn2/S1 simultaneously supports evidence of its role as a ubiquitin receptor. Finally, when complexed to di-ubiquitin, via the Pru, and Uch37 via the C-terminal part, it frees up the distal ubiquitin for de-ubiquitination by the Uch37 .
BAF1 / ABF1 chromatin reorganising factor (BAF1_ABF1)
Type: Family

ABF1 (ARS-binding factor 1) is a sequence-specific DNA binding protein involved in transcription activation, gene silencing and initiation of DNA replication. ABF1 is known to remodel chromatin, and it is proposed that it mediates its effects on transcription and gene expression by modifying local chromatin architecture . These functions require a conserved stretch of 20 amino acids in the C-terminal region of ABF1 (amino acids 639 to 662 Saccharomyces cerevisiae (

)) . The N-terminal two thirds of the protein are necessary for DNA binding, and the N terminus (amino acids 9 to 91 in S. cerevisiae) is thought to contain a novel zinc-finger motif which may stabilise the protein structure .
Glycosyl-hydrolase family 116, catalytic region (GH116_catalytic)
Type: Domain

This entry represents the catalytic region found in the CAZyme GH116 family members, which presently includes enzymes with beta-glucosidase (

), beta-xylosidase (

) , and glucocerebrosidase (

) activity . Proteins containing this domain include animal non-lysosomal glucosylceramidase GBA2, which catalyse the conversion of glucosylceramide to free glucose and ceramide . GBA2 is involved in sphingomyelin generation and prevention of glycolipid accumulation and may also catalyse the hydrolysis of bile acid 3-O-glucosides, however, the relevance of such activity is unclear in vivo . Mutations in the human protein cause motor-neurone defects in hereditary spastic paraplegia . The catalytic nucleophile, identified in

is a glutamine-335, with the likely acid/base at Asp-442 and the aspartates at Asp-406 and Asp-458 residues also playing a role in the catalysis of glucosides and xylosides that are beta-bound to hydrophobic groups .
Sporulation-specific cell division protein SsgB (SsgB)
Type: Family

SsgB is a conserved activator of developmental cell division in morphologically complex actinomycetes . It controls cell division and spore maturation in streptomycetes. Together with SsgA, SsgB activates sporulation-specific cell division by controlling the localisation of FtsZ .

SsgB shows structural similarity to whirly ssDNA/guide RNA-binding proteins found in mitochondria or in plants, but the interaction of this protein with nucleic acids is unlikely. On the other hand, a conserved surface for protein-protein interaction has been identified and suggest that SsgB might be a binding partner .
Minor spike protein (Microvir_H)
Type: Family

This entry represents the minor spike protein (also known as H protein), which is a minor spike component of the viral shell. It is involved in the ejection of the phage DNA in the host and is injected with the DNA in the periplasmic space of the host. It is involved in the determination of the phage host-range .
DNA binding protein S1FA (S1FA_DNA-bd)
Type: Family

S1FA is an unusual small plant peptide of only 70 amino acids with a basic domain which contains a nuclear localization signal and a putative DNA binding helix. S1FA is highly conserved between dicotyledonous and monocotyledonous plants and may be a DNA-binding protein that specifically recognises the negative promoter element S1F .
YABBY protein (YABBY)
Type: Family

YABBY proteins are a group of plant-specific transcription factors involved in diverse aspects of leaf, shoot and flower development .
Apolipoprotein C-I (ApoC-I)
Type: Family

Exchangeable apolipoproteins are water-soluble protein components of lipoproteins that solubilise lipids and regulate their metabolism by binding to cell receptors or activating specific enzymes. Apolipoprotein C-I (ApoC-1) is the smallest exchangeable apolipoprotein and transfers among HDL (high density lipoprotein), VLDL (very low-density lipoprotein) and chlylomicrons. ApoC-1 activates lecithin:choline acetyltransferase (LCAT), inhibits cholesteryl ester transfer protein, can inhibit hepatic lipase and phospholipase 2 and can stimulate cell growth. ApoC-1 delays the clearance of beta-VLDL by inhibiting its uptake via the LDL receptor-related pathway . ApoC-1 has been implicated in hypertriglyceridemia , and Alzheimer s disease .

ApoC-1 is believed to comprise of two dynamic helices that are stabilised by interhelical interactions and are connected by a short linker region. The minimal folding unit in the lipid-free state of this and other exchangeable apolipoproteins comprises the helix-turn-helix motif formed of four 11-mer sequence repeats.
Platelet-derived growth factor, N-terminal (PDGF_N)
Type: Domain

Platelet-derived growth factor (PDGF) is a potent mitogen for cells of mesenchymal origin, including smooth muscle cells and glial cells. In both mouse and human, the PDGF signalling network consists of four ligands, PDGFA-D, and two receptors, PDGFRalpha and PDGFRbeta. All PDGFs function as secreted, disulphide-linked homodimers, but only PDGFA and B can form functional heterodimers. PDGFRs also function as homo- and heterodimers. All known PDGFs have characteristic `PDGF domains', which include eight conserved cysteines that are involved in inter- and intramolecular bonds. Alternate splicing of the A chain transcript can give rise to two different forms that differ only in their C-terminal extremity. The transforming protein of Woolly monkey sarcoma virus (WMSV) (Simian sarcoma virus), encoded by the v-sis oncogene, is derived from the B chain of PDGF.

PDGFs are mitogenic during early developmental stages, driving the proliferation of undifferentiated mesenchyme and some progenitor populations. During later maturation stages, PDGF signalling has been implicated in tissue remodelling and cellular differentiation, and in inductive events involved in patterning and morphogenesis. In addition to driving mesenchymal proliferation, PDGFs have been shown to direct the migration, differentiation and function of a variety of specialised mesenchymal and migratory cell types, both during development and in the adult animal .

PDGF is structurally related to a number of other growth factors which also form disulphide-linked homo- or heterodimers.

This domain consists of the N-terminal regions of PGDF A and B.
Transposase, ISC1217 (Transposase_ISC1217)
Type: Family

Autonomous mobile genetic elements such as transposon or insertion sequences (IS) encode an enzyme, transposase, that is required for excising and inserting the mobile element. Transposases have been grouped into various families . This family includes the putative transposase ISC1217 from archaebacteria.
Coronavirus Orf3 (Coronavirus_Orf3)
Type: Family

This family represents the Coronavirus ORF3 protein, also known as the X2A protein.
Peroxisome membrane anchor protein Pex14p, N-terminal (Pex14_N)
Type: Domain

This conserved region defines a group of peroxisomal membrane anchor proteins which bind the PTS1 (peroxisomal targeting signal) receptor and are required for the import of PTS1-containing proteins into peroxisomes. Loss of functional Pex14p results in defects in both the PTS1 and PTS2-dependent import pathways. Deletion analysis of this conserved region implicates it in selective peroxisome degradation. In the majority of members this region is situated at the N terminus of the protein .
Pinin/SDK/MemA protein (Pinin_SDK_MemA)
Type: Domain

This conserved region is located adjacent and C-terminal to a N-terminal pinin/SKD domain

. Members of this family have very varied localisations within the eukaryotic cell. Pinin is known to localise at the desmosomes and is implicated in anchoring intermediate filaments to the desmosomal plaque . SDK2/3 is a dynamically localised nuclear protein thought to be involved in modulation of alternative pre-mRNA splicing . MemA is a tumour marker preferentially expressed in human melanoma cell lines. A common feature of the members of this family is that they may all participate in regulating protein-protein interactions .
Pinin/SDK (Pinin_SDK_N)
Type: Domain

This conserved region is found at the N-terminal of the member proteins. It is located adjacent and N-terminal to the pinin/SKD/memA domain

. Members of this family have very varied localisations within the eukaryotic cell. Pinin is known to localise at the desmosomes and is implicated in anchoring intermediate filaments to the desmosomal plaque . SDK2/3 is a dynamically localised nuclear protein thought to be involved in modulation of alternative pre-mRNA splicing . MemA is a tumour marker preferentially expressed in human melanoma cell lines. A common feature of the members of this family is that they may all participate in regulating protein-protein interactions .
Rab effector MyRIP/Melanophilin (Myrip/Melanophilin)
Type: Domain

This domain is found in Rab effector MyRIP and melanophilin. They are both Rab effector proteins involved in melanosome transport .
Actin-related protein 2/3 complex subunit 5 (ARPC5)
Type: Family

Arp2/3 binds to pre-existing actin filaments and nucleates new daughter filaments, and thus becomes incorporated into the dynamic actin network at the leading edge of motile cells and other actin-based protrusive structures . In order to nucleate filaments, Arp2/3 must bind to a member of the N-WASp/SCAR family protein . Arp2 and Arp3 are thought to be brought together after activation, forming an actin-like nucleus for actin monomers to bind and create a new actin filament. In the absence of an activating protein, Arp2/3 shows very little nucleation activity. Recent research has focused on the binding and hydrolysis of ATP by Arp2 and Arp3 , and crystal structures of the Arp2/3 complex have been solved .

The human Arp2/3 complex consists of ARP2, ARP3, ARPC1B/p41-ARC, ARPC2/p34-ARC, ARPC3/p21-ARC, ARPC4/p20-ARC and ARPC5/p16-ARC. This family represents the ARPC5/p16-ARC subunit.
Baculovirus Gp41, glycoprotein (Baculovirus_Gp41)
Type: Family

This is a family of viral structural glycoproteins from the baculoviridae.
Pox virus D2 protein (Pox_D2)
Type: Family

This entry represents the Pox virus D2 proteins, also known as OPG114. D2 is a late protein which is part of a large complex required for early virion morphogenesis. This complex participates in the formation of virosomes and the incorporation of virosomal contents into nascent immature virions .
Vicilin, N-terminal (Vicilin_N)
Type: Domain

This region is found in plant seed storage proteins, N-terminal to the Cupin domain (

). In Macadamia integrifolia (Macadamia nut) (

), this region is processed into peptides of approximately 50 amino acids containing a C-X-X-X-C-(10-12)X-C-X-X-X-C motif. These peptides exhibit antimicrobial activity
in vitro
.
FaeA-like protein (FaeA)
Type: Family

This family represents a number of fimbrial protein transcription regulators found in Gram-negative bacteria. These proteins are thought to facilitate binding of the leucine-rich regulatory protein to regulatory elements, possibly by inhibiting deoxyadenosine methylation of these elements by deoxyadenosine methylase .
Transcriptional activator, Zfx/Zfy domain (Transcrp_activ_Zfx/Zfy-dom)
Type: Domain

Zfx and Zfy are transcription factors implicated in mammalian sex determination. This region is found N-terminal to multiple copies of a C2H2 Zinc finger. This region has been shown to activate transcription when fused to a GAL4 DNA binding domain .
Thiostrepton-resistance methylase, N-terminal (Thiostrepton-R_Mease_TSNR_N)
Type: Domain

This region is found in some members of the SpoU-type rRNA methylase family (

).
Dickkopf, N-terminal cysteine-rich (Dickkopf_N)
Type: Domain

Dickkopf proteins are a class of Wnt antagonists. They possess two conserved cysteine-rich regions. This entry represents the N-terminal conserved region . This domain, as its C-terminal region, have been found to share significant sequence similarity to the colipase fold (

) .
PRELI/MSF1 domain (PRELI/MSF1_dom)
Type: Domain

The PRELI/MSF1 domain is an eukaryotic protein module which occurs in stand- alone form in several proteins, including the human PRELI protein and the yeast MSF1 protein, and as an amino-terminal domain in an orthologous group of proteins typified by human SEC14L1, which is conserved in all animals. In this group of proteins, the PRELI/MSF1 domain co-occurs with the CRAL-TRIO and the GOLD domains. The PRELI/MSF1 domain is approximately 170 residues long and is predicted to assume a globular α + β fold with six β strands and four α helices. It has been suggested that the PRELI/MSF1 domain may have a function associated with cellular membrane .
Poxvirus F16 (Poxvirus_F16)
Type: Family

This entry represents the Poxvirus F16 proteins, also known as Protein OPG061. This protein is expressed in the early phase of the viral replicative cycle .
Anti-Mullerian hormone, N-terminal (AMH_N)
Type: Domain

Anti-Mullerian hormone, AMH is a signalling molecule involved in male and female sexual differentiation . Defects in synthesis or action of AMH cause persistent Mullerian duct syndrome (PMDS), a rare form of male pseudohermaphroditism . This family represents the N-terminal part of the protein, which is not thought to be essential for activity . AMH contains a TGF-beta domain (

), at the C terminus.
Pellino family (Pellino_fam)
Type: Family

Pellino proteins are E3 ubiquitin ligases that play an important role in immunity . Pellinos contain a CHC2CHC2 RING E3 ubiquitin ligase domain . Mammalian Pellinos have been shown to mediate polyubiquitination of interleukin-1 receptor-associated kinase (IRAK) .
Apolipoprotein A-II (ApoA-II) (ApoA-II)
Type: Family

Apolipoprotein A-II (ApoA-II) is the second major apolipoprotein of high density lipoprotein in human plasma. Mature ApoA-II is present as a dimer of two 77-amino acid chains joined by a disulphide bridge . ApoA-II regulates many steps in HDL metabolism, and its role in coronary heart disease is unclear . In bovine serum, the ApoA-II homologue is present in almost free form. Bovine ApoA-II shows antimicrobial activity against Escherichia coli and yeasts in phosphate buffered saline (PBS) .
Radial spokehead-like protein (Radial_spoke)
Type: Family

This family includes the radial spoke head proteins RSP4 and RSP6 from Chlamydomonas reinhardtii, and several eukaryotic homologues, including mammalian RSHL1, the protein product of a familial ciliary dyskinesia candidate gene . The radial spoke head proteins are important in maintaining normal movement in motile, "9+2"-structure cilia and flagella. Mutations of the human RSPH9 and RSPH4A genes have been linked to primary ciliary dyskinesia, a genetically heterogeneous inherited disorder arising from dysmotility of motile cilia and sperm . RSPH6A has also been shown to be required for sperm flagellum formation and male fertility in mice .
Poxvirus I5 (Poxvirus_I5)
Type: Family

This entry represents the Poxvirus protein I5, also known as Protein OPG081. In Vaccinia virus, I5 is associated with the membranous components of assembling and mature virions .
BCL7 (BCL7)
Type: Family

The members of this group of sequences contain a conserved N-terminal domain which is found in the BCL7 family. Human BCL7 family consists of BCL7A, BCL7B, and BCL7C. They are involved in cancer incidence, progression, and development. BCL7B is commonly hemizygously deleted in patients with Williams syndrome . BCL7B regulates several signalling pathways including Wnt and apoptosis .
Anthranilate synthase component I, N-terminal (Anth_synth_I_N)
Type: Domain

Anthranilate synthase catalyses the first step in the biosynthesis of tryptophan. Component I catalyses the formation of anthranilate using ammonia and chorismate. The catalytic site lies in the adjacent region, described in the chorismate binding enzyme family (

). This region is involved in feedback inhibition by tryptophan . This family also contains a region of Para-aminobenzoate synthase component I.
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5 (NDUFA5)
Type: Family

NDUFA5, also known as NADH-ubiquinone oxidoreductase 13kDa-B subunit, is an accessory subunit of the mitochondrial membrane respiratory chain NADH dehydrogenase (Complex I) .
ATP synthase F0 complex subunit G, mitochondrial (ATP_synth_F0_gsu_mt)
Type: Family

This entry represents the G subunit found in the F0 complex of F-ATPases in mitochondria. The function of subunit G is currently unknown. There is no counterpart in chloroplast or bacterial F-ATPases identified so far .

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.
TAFII28-like protein domain (TAFII28_dom)
Type: Domain

The general transcription factor, TFIID, consists of the TATA-binding protein (TBP) associated with a series of TBP-associated factors (TAFs) that together participate in the assembly of the transcription preinitiation complex. This entry represents a conserved domain found at the C terminus of Transcription initiation factor TFIID subunit 11 from humans (also known as Transcription initiation factor TFIID 28 kDa subunit, TAFII28 ). TAF11 interacts with the ligand binding domains of the nuclear receptors for vitamin D3 and thyroid hormone . It also interacts directly with TFIIA, acting as a bridging factor that stabilises the TFIIA-TBP-DNA complex . The crystal structure of hTAFII28 with hTAFII18 shows that this region is involved in the binding of these two subunits. The conserved region contains four α-helices and three loops arranged as in histone H3 .
RNA polymerase II subunit A (RNA_pol_II_suA)
Type: Family

The highly conserved and essential protein Ssu72 has intrinsic phosphatase activity and plays an essential role in the transcription cycle. Ssu72 was originally identified in a yeast genetic screen as enhancer of a defect caused by a mutation in the transcription initiation factor TFIIB . It binds to TFIIB and is also involved in mRNA elongation. Ssu72 is further involved in both poly(A) dependent and independent termination. It is a subunit of the yeast cleavage and polyadenylation factor (CPF), which is part of the machinery for mRNA 3'-end formation. Ssu72 is also essential for transcription termination of snRNAs .
Glycine reductase complex selenoprotein A (GRDA)
Type: Family

Found in clostridia, this protein contains one active site selenocysteine and catalyses the reductive deamination of glycine, which is coupled to the esterification of orthophosphate resulting in the formation of ATP . A member of this family may also exist in Treponema denticola .
Glycosyl transferase, family 17 (Glyco_trans_17)
Type: Family

This family represents beta-1,4-mannosyl-glycoprotein beta-1,4-N-acetylglucosaminyltransferase (

). This enzyme transfers the bisecting GlcNAc to the core mannose of complex N-glycans. The addition of this residue is regulated during development and has functional consequences for receptor signalling, cell adhesion, and tumour progression .