SII-SWORD/CoKE huggingface dataset:
PCNA-associated factor, histone-like domain (PCNA-AF_dom)
Type: Domain

PCNA-associated factor or p15PAF is a nuclear protein first identified as a proliferating-cell-nuclear-antigen (PCNA)-binding protein . As a direct transcriptional target of activating transcription factor 3 (ATF3) it is involved in maintaining genomic integrity after UV exposure . It is also a direct transcriptional target of the Rb/E2F pathway, playing an essential role in DNA synthesis and cell cycle progression . p15PAF/KIAA0101 is overexpressed in multiple types of human cancer .

This domain corresponds to a histone-like fold in p15(PAF).
Protein of unknown function DUF4672 (DUF4672)
Type: Family

This family of proteins is found in chordates. Proteins in this family are typically between 165 and 199 amino acids in length.
Pericentriolar material 1 protein, C-terminal (PCM1_C)
Type: Domain

This entry represents the C-terminal domain of pericentriolar material 1 (PCM1), a protein involved in the assembly of centrosomal proteins and microtubule organisation .
Protein moonraker (MNR)
Type: Family

This entry represents protein moonraker (MNR) from animals. MNR is a centriolar satellite component involved in centriole duplication. It promotes centriole duplication by localizing WDR62 to the centrosome .
Annexin-2 receptor (ANXA2R)
Type: Family

Annexin-2 is a heterotetramer that is produced by osteoclasts and stimulates osteoclast formation. This family of proteins acts as annexin-2 receptors (ANXA2R, AXIIR) . Besides being a cell surface receptor of annexin-2, AXIIR can also be located in cytoplasm and act as an activator of apoptosis in human cells .
Poxin-Schlafen/Schlafen-like, N-terminal domain (Poxin-SLFN/SLFN_N)
Type: Domain

This entry represents a domain found at the N-terminal of Schlafen and Schlafen-like proteins such B3 protein from Orthopoxvirus and poxin-Schlafen from Cowpox virus. It is a nuclease responsible for viral evasion of host cGAS-STING innate immunity .
mRNA interferase toxin MqsR (MqsR_toxin)
Type: Family

MqsR is a bacterial toxin that acts as an mRNA interferase . MqsR is the gene most highly upregulated in E. coli persister cells and it plays an essential role in biofilm regulation and cell signalling . It forms part of a bacterial toxin-antitoxin TA system, and as expected for a TA system, the expression of the MqsR toxin leads to growth arrest, while co-expression with its antitoxin, MqsA, rescues the growth arrest phenotype. In addition, MqsR associates with MqsA to form a tight, non-toxic complex and both MqsA alone and the MqsR:MqsA2:MqsR complex bind and regulate the mqsR promoter. The structure of MqsR shows that it is a member of the RelE/YoeB family of bacterial RNases that are structurally and functionally characterised bacterial toxins .
Protein Kre1 (Kre1)
Type: Family

Killer toxin-resistance protein 1 (kre1) is a GPI-anchored plasma membrane protein. It is involved in the late stage of cell wall 1,6-beta-glucan synthesis and assembly . Its function in yeast cell wall assembly is structural, rather than enzymatic. It can also act as a plasma membrane receptor for the yeast K1 viral toxin, and is involved in subsequent lethal channel formation . This entry also includes Pga1 protein, which has a role in oxidative stress response and is required for normal adhesion to host cells and for adherence during biofilm formation .
Transmembrane protein 119 (TMEM119)
Type: Family

Tmem119 is an osteoblast induction factor, also known as Obif, which encodes a single transmembrane protein. It promotes the differentiation of myoblasts into osteoblasts , and plays an essential role in bone formation by regulating osteoblastogenesis .
Viral matrix protein M (Viral_M)
Type: Family

This entry includes matrix proteins from Nucleorhabdovirus. They may play a major role in assembly and budding of virion.
Genetic interactor of prohibitin 5 (Gep5)
Type: Family

Genetic interactor of prohibitin 5 (Gep5) was identified as a mitochondrial genome maintenance protein from a genome-wide screen . It has been shown to interact with prohibitin ring complexes in the mitochondrial inner membrane . Gep5 is detected in highly purified mitochondria in high-throughput studies . The function of Gep5 is not clear.
Cap-associated protein Caf20 (Caf20)
Type: Family

In eukaryotes, the translation of mRNA is initiated by the binding of eIF4F complex, which is composed of eIF4E, eIF4A and eIF4G proteins. elF4E-binding proteins (4E-BPs) are involved in translational regulation through their interaction with eIF4E. There are two elF4E-binding proteins (4E-BPs) found in S. cerevisiae, Caf20 and Eap1 .

This entry represents Caf20 (also known as p20), which competes with elF4G for binding to elF4E and interferes with the formation of the elF4F complex, hence inhibiting translation . Caf20 is needed for the induction of pseudohyphal growth in response to nitrogen limitation .
Renal cancer differentiation gene 1 protein (RCDG1)
Type: Family

This family includes human protein C4orf46, also known as renal cancer differentiation gene 1 protein (RCDG1) .
Protein of unknown function DUF4677 (DUF4677)
Type: Family

This uncharacterised family is also known as coiled-coil domain-containing protein 184 (CCDC184).
Cytochrome c oxidase assembly factor 2 (Coa2)
Type: Family

Coa2 is a cytochrome oxidase assembly factor required for efficient assembly of cytochrome c oxidase in the mitochondrial inner membrane. It may aid in stabilising an early Cox1 intermediate containing the nuclear subunits Cox5A and Cox6 .
Protein of unknown function DUF4678 (DUF4678)
Type: Family

This family of proteins includes the uncharacterised testis-expressed protein 44 (in humans, the protein is a product of C2orf57). Proteins in the family are found in chordates and are typically between 318 and 395 amino acids in length.
Protein of unknown function DUF4679 (DUF4679)
Type: Family

Proteins in this family are typically between 213 and 412 amino acids in length and are found in chordates. They are also known as proline-rich protein 30.
Cation channel sperm-associated targeting subunit tau (CTSRT)
Type: Family

Cation channel sperm-associated targeting subunit tau (CTSRT, also known as Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 11 and C2 calcium-dependent domain-containing protein 6) has been identified in mice as an auxiliary component of the CatSper complex, which is involved in sperm cell hyperactivation. Sperm cell hyperactivation is required for sperm motility, essential late in the preparation of sperm for fertilization . This protein is key for CatSper flagellar targeting and trafficking into the quadrilinear nanodomains as it links the channel-carrying vesicles and motor proteins in elongating flagella.
MICOS complex subunit Mic12 (Mic12)
Type: Family

Mic12, also known as Aim5, is a subunit of the MICOS complex, a mitochondrial inner membrane complex that functions as a primary determinant of mitochondrial inner membrane structure .

Yeast MICOS complex is comprised of six core subunits: Mic60, Mic10, Mic19, Mic27, Mic26, and Mic12. The MICOS complex can be divided into two independent subcomplexes: Mic27/Mic10/Mic12 and Mic60/Mic19 according to their dependence of respiratory complexes and the mitochondrial lipid cardiolipin. The dependence of the Mic27/Mic12/Mic10 subcomplex on respiratory complexes suggests that in addition to the roles in cristae biogenesis, this subcomplex coordinates with respiratory complexes and lipids to establish mitochondrial inner membrane architecture .
Protein of unknown function DUF4680 (DUF4680)
Type: Family

This family of proteins is found in eukaryotes. Proteins in this family are typically between 65 and 178 amino acids in length. There are two conserved sequence motifs: VISRM and ENE.
Protein of unknown function DUF4681 (DUF4681)
Type: Family

This family of proteins is found in chordates and includes human uncharacterised protein C12orf54. Proteins in this family are typically between 101 and 127 amino acids in length.
Migration and invasion-inhibitory protein (MIIP)
Type: Family

Migration and invasion-inhibitory protein (MIIP or IIp45) binds to insulin-like growth factor binding protein 2 (IGFBP-2) and inhibits the invasion of glioma cells . MIIP attenuates mitotic transition, thereby inhibiting glioma progression . It not only modulates IGFBP-2, but also inhibits cell migration by binding to and inhibiting HDAC6, a class 2 histone deacetylase that deacetylates alpha-tubulin .
ATPase expression protein 1 (Aep1)
Type: Family

Aep1 is a mitochondrial protein required for expression of the mitochondrial OLI1 gene, which encodes F1-F0 ATP synthase subunit 9 .
Synaptotagmin-like mitochondrial-lipid-binding domain (SMP_LBD)
Type: Domain

Membrane contacts sites (MCSs), regions where two organelles come in close proximity to one another, act as molecular hubs for the exchange of small molecules (e.g. lipids) and signals (e.g. calcium ions). Synaptotagmin-like Mitochondrial lipid-binding Proteins (SMP) domains are exclusively found at MCSs between different organelles such as endoplasmic reticulum (ER)- Mitochondrion, ER-Plasma membrane (PM) and Nucleus-Vacuole junctions. The SMP domain is able to homo- or heterodimerize, harbors lipids in a hydrophobic cavity and mediates lipid transfer between the two adjacent bilayers independently of membrane fusion and fission reactions. SMP proteins are widespread amongst eukaryotic species with a particular enrichment in plants and features suggestive of species-specific functional variations. SMP domain- containing proteins have been classified into four broad groups: C2 domain synaptotagmin-like, PH domain-containing HT-008, PDZK8 and mitochondrial protein families .

The SMP domain consists of 6 β-strands and 3 helices arranged to form a barrel whose interior is lined almost exclusively by hydrophobic residues. The resulting elongated barrel-shaped cylindrical structure harbors a lateral opening and a central hydrophobic cavity where phospholipids can bind. It dimerizes in an anti-parallel fashion to form a cylinder traversed by a deep hydrophobic groove . The SMP domain belongs to the TULIP (for TUbular LIPid-binding) protein superfamily of lipid transfer proteins .
Fungal death-pathway protein, SesB domain (SesB_dom)
Type: Domain

This entry represents a short conserved domain found in fungal proteins that are part of the cell death or heterokaryon incompatibility pathway .
CEP63/Deup1, N-terminal (CEP63/Deup1_N)
Type: Domain

This entry represents the N-terminal domain of the human centrosomal protein 63 kDa (Cep63), its paralogue Deuterosome assembly protein 1 (Deup1).

CEP63 and Deup1 are both involved in centriole amplification. While CEP63 mediates mother-centriole-dependent centriole duplication, Deup1 mediates de novo centriole amplification in multiciliated cells .
Protein BptA (BptA)
Type: Family

BptA family members are found in Borrelia species. Borrelia burgdorferi BptA is a virulence-associated protein essential for survival of the bacterium within the tick host, and therefore within the natural life cycle of the Lyme disease spirochete .
MAT1-1-2/MatA-2/Smr1 (MAT1-1-2/MatA-2/Smr1)
Type: Family

This entry includes MAT1-1-2, MatA-2 and Smr1 from Sordariomycetes.
Protein of unknown function DUF4684 (DUF4684)
Type: Family

This family of proteins is found in chordates. Proteins in this family are typically between 531 and 1277 amino acids in length.
Protein phosphatase 1 regulatory subunit 26, N-terminal domain (PPP1R26_N)
Type: Domain

This entry represents the N-terminal domain of protein phosphatase 1 regulatory subunit 26 .
Four-carbon acid sugar kinase, nucleotide binding domain (NBD_C)
Type: Domain

This is the C-terminal domain found in proteins in a range of Proteobacteria as well as the Gram-positive Oceanobacillus iheyensis. Structural analysis of the whole protein indicates the N- and C-termini act together to produce a surface into which a threonate-ADP complex is bound, demonstrating that a sugar binding site is on the N-terminal domain, and a nucleotide binding site is in the C-terminal domain . There is a critical motif, DDXTG, at approximately residues 22-25. Proteins containing this domain have been predicted as kinases. Some members are associated with PdxA2 by physical clustering and gene fusion with PdxA2. Some members that are fused with PdxA2 have been shown to be involved in L-4-hydroxythreonine (4HT) phosphorylation, part of the alternative pathway to make PLP (pyridoxal 5'-phosphate) out of a toxic metabolite, 4HT. However, 4HT phosphorylation might not be the main function of this group of proteins. Moreover, some members that are not associated with pdxA2, and even one that is associated with pdxA2, have lost 4HT kinase activity . Functional analysis demonstrate that family members include D-Threonate kinases (DtnK), D-Erythronate kinases (DenK) and 3-Oxo-tetronate kinases (OtnK) .
Protein of unknown function DUF4686 (DUF4686)
Type: Family

This family includes proteins described as coiled-coil domain-containing protein 30. Proteins in this family are typically between 498 and 775 amino acids in length. There is a conserved DLK sequence motif.
E domain (SasG_E)
Type: Domain

This short domain is about 50 amino acids in length. Its structure shows that it is composed of two β sheets each of three strands. This domain is found associated with the G5 domain (

) and has structural similarity with G5 domain, although it is somewhat shorter . The E domain forms part of a rod like structure.
Spermatogenesis-associated protein 1, C-terminal domain (SPATA1_C)
Type: Domain

The spermatogenesis associated 1 (SPATA1) protein is thought to be involved in spermatogenesis and is a potential marker for male fertility . This entry represents the C-terminal domain of SPATA1.
Protein SLX4IP (SLX4IP)
Type: Family

SLX4IP (SLX4-interacting protein) encodes an uncharacterised DNA repair-related protein . Deletions of SLX4IP have been associated with childhood lymphoblastic leukemia .
Cellulose-complementing protein (CcpAX)
Type: Family

This entry represents the bacterial cellulose-complementing protein proteins, which are necessary for cellulose biosynthesis. Cellulose is necessary for biofilm formation in bacteria .
Fucosyltransferase, N-terminal (Glyco_tran_10_N)
Type: Domain

This is the N-terminal domain of a family of fucosyltransferases, known as glycosyltransferase family 10 . This enzyme transfers fucose from GDP-Fucose to GlcNAc in an alpha1,3 linkage . The N-terminal domain folds as a Rossmann-like domain and is involved in sugar donor interactions .
Cellulose biosynthesis protein BcsN (CBP_BcsN)
Type: Family

This is a family of bacterial cellulose biosynthesis proteins. Cellulose is necessary for biofilm formation in bacteria .
AP-1 complex-associated regulatory protein (AP1AR)
Type: Family

AP-1 complex-associated regulatory protein (AP1AR), also known as gadkin or gamma-BAR, is a negative regulator of the actin-related protein (ARP)2/3 complex, a major regulator of actin dynamics. Through inhibition of ARP2/3, gadkin negatively regulates cell spreading and motility . Gadkin is also a modulator of adaptor protein (AP)-1-mediated endosomal membrane trafficking .
Cellulose biosynthesis protein BcsO (CBP_BcsO)
Type: Family

BcsO is a family of bacterial cellulose biosynthesis proteins. Cellulose is necessary for biofilm formation in bacteria .
Cellulose biosynthesis protein BcsS (CBP_BcsS)
Type: Family

BcsS is a family of bacterial cellulose biosynthesis proteins. Cellulose is necessary for biofilm formation in bacteria .
Transmembrane protein 215 (TMEM215)
Type: Family

This family of proteins is found in eukaryotes. Proteins in this family are approximately 230 amino acids in length.
Protein of unknown function DUF4687 (DUF4687)
Type: Family

This family includes uncharacterised protein C11orf71. Proteins in this family are typically between 76 and 140 amino acids in length.
GATOR2 complex protein MIO, zinc-ribbon like domain (Zn_ribbon_mio)
Type: Domain

This entry represents the zinc-ribbon-like domain found in the C-terminal end of the GATOR complex protein MIOS (also known as WD40 repeat containing protein mio). MIOS is a component of the GATOR subcomplex GATOR2, a complex which positively regulates mTORC1 signalling by acting upstream of or in parallel to GATOR1 . GATOR1 complex is a major negative regulator of the amino acid sensing pathway and its loss causes mTORC1 signalling to be completely insensitive to amino acid starvation .
D,L-carboxypeptidase, peptidase domain (Peptidase_M99)
Type: Domain

This is the peptidase domain of a D,L-carboxypeptidase. The active site residues are Arg86, Glu222 and the metal ligands, in the peptidase domain, are Gln46, Glu49 and His128 in

. The protein binds many zinc ions and a calcium ion and there are other metal binding sites. The catalytic activity is the release of m-Dpm from the peptide muramyl-Ala-gamma-D-Glu-m-Dpm; this is probably the precursor of the cell wall cross-linking peptide .
FAAP20, zinc finger UBZ2-type (UBZ2_FAAP20)
Type: Domain

The ubiquitin-binding zinc finger (UBZ) is a type of zinc-coordinating β-β-α fold domain found mainly in proteins involved in DNA repair and transcriptional regulation. UBZ domains coordinate a zinc ion with cysteine or histidine residues; depending on their amino acid sequence, UBZ domains are classified into several families . Type 1 UBZs are CCHH-type zinc fingers found in tandem UBZ domains of TAX1-binding protein 1 (TAX1BP1) , type 2 UBZs are CCHC-type zinc fingers found in FAAP20 which is a subunit of the Fanconi anemia (FA) core complex , type 3 UBZs are CCHH-type zinc fingers found only in the Y-family translesion polymerase eta , and type 4 UBZs are CCHC-type zinc fingers found in Y-family translesion polymerase kappa, Werner helicase-interacting protein 1 (WRNIP1), and Rad18 .

This domain is the type 2 UBZ found in Fanconi anemia-associated protein of 20kDa (FAAP20) .
FAAP20, FANCA interaction domain (FANCA_interact)
Type: Domain

This domain is found in the N-terminal of Fanconi anemia-associated protein of 20kDa (FAAP20), where it is responsible for interaction with Fanconi anemia group A protein (FANCA) .

The Fanconi anemia (FA) pathway participates in interstrand cross-link repair and the maintenance of genomic stability. FAAP20 is a component of the FA core complex.
Protein of unknown function DUF5101 (DUF5101)
Type: Family

This is a family of short microsporidia-specific proteins of unknown function.
Zinc-ribbon 15 (Zinc_ribbon_15)
Type: Domain

This zinc-ribbon region is found, among others, in many microsporidia proteins.
Putative beta-lactamase-like family (Beta_lactamase3)
Type: Family

This is a family derived from microsporidia-specific proteins. There is homology to the beta-lactamase domain .
Protein of unknown function DUF5100 (DUF5100)
Type: Family

This is a family of microsporidia-specific proteins of unknown function.
Protein of unknown function DUF4688 (DUF4688)
Type: Family

This family of proteins is found in eukaryotes. Proteins in this family are typically between 331 and 596 amino acids in length.
Microsporidial 8TM transmembrane domain (8TM_micro)
Type: Domain

This entry represents the eight transmembrane regions (in two blocks of four) of microsporidial-specific proteins. Such an arrangement of TMs suggests a transporter function of some kind. There is a highly conserved NFLNW sequence-motif at the C terminus which might be of functional importance .
Bromodomain associated protein-like (Bromo_TP-like)
Type: Family

This is a family of microsporidia-specific proteins that have distant homology to the Bromodomain associated domain (

).
Protein of unknown function DUF4689 (DUF4689)
Type: Family

This family of proteins is found in eukaryotes. Proteins in this family are typically between 202 and 224 amino acids in length.
Protein SNORC (SNORC)
Type: Family

SNORC is a cartilage specific small membrane proteoglycan that plays a role in the regulation of chondrocyte maturation and postnatal endochondral ossification .
Amelotin (Amelotin)
Type: Family

Amelotin (AMTN) is specifically expressed during the maturation stage of dental enamel formation . It plays a role in dental enamel formation by promoting hydroxyapatite mineralisation .
Putative zinc-finger ribonucleoprotein (Zf_ribonucleo)
Type: Family

This is a family of microsporidia-specific proteins . One member is annotated as being a ribonucleoprotein . The family carries two pairs of CxxC residues suggesting that there is DNA-binding.
Protein of unknown function DUF5099 (DUF5099)
Type: Family

This is a family of microsporidia-specific sequences with unknown function.
Putative DMAP1-like (DMAP1-like)
Type: Family

This is a family of microsporidia-specific proteins that may have distant homology to the family DMAP1 (

).
Protein of unknown function DUF5098 (DUF5098)
Type: Family

This entry represents a group of microsporidia-specific proteins with no known function. There is a very characteristic NPW sequence motif at the very C terminus.
Histidine-rich carboxyl terminus protein 1 (HRCT1)
Type: Family

The function of this family of proteins is not known.
Polar tube protein 2 (PTP2)
Type: Family

This entry represents polar-tube protein 2 from Microsporidia. Humans can be infected with the unicellular eukaryote Microsporidia which are obligate intracellular parasites that produce resistant spores. To initiate entry into a new host cell a unique motile process is formed by a sudden extrusion of the polar tube protein from the spore . There are a series of conserved cysteine residues.
Transmembrane protein 108 (TMEM108)
Type: Family

This family of proteins is found in eukaryotes. Proteins in this family are typically between 258 and 575 amino acids in length.
Putative double-strand recombination repair protein-like (Mei5-like)
Type: Family

This is a family of microsporidia-specific sequences with homology to the double-strand recombination repair protein family (

).
Leukemia-associated protein 7 (DLEU7)
Type: Family

Leukemia-associated protein 7 (DLEU7 or LEU7) is a gene of unknown function deleted in lymphocytic leukemia . It is a vertebrate-specific gene that might have a role in development .
Domain of unknown function DUF5097 (DUF5097)
Type: Domain

This entry represents a domain found in a group of microsporidia-specific proteins of unknown function. There is the possibility of very distant homology to the WAC domain.
Domain of unknown function DUF5096 (DUF5096)
Type: Domain

This entry represents a domain found in a group of microsporidial proteins of unknown function. There is a well conserved Asp residue towards the C terminus which may be functional.
Spore wall protein (MICSWaP)
Type: Family

This is a family of microsporidial spore-wall proteins .
Aberrant zinc-finger domain (Zf-C2H2_aberr)
Type: Domain

This represents an aberrant zinc-finger motif of Cx(4)C2H repeated found in a group of largely microsporidia-specific proteins.
Protein of unknown function DUF5095 (DUF5095)
Type: Family

This entry represents a family of microsporidial-specific sequences. The function is not known.
Protein of unknown function DUF4691 (DUF4691)
Type: Family

This family of proteins is found in chordates. Proteins in this family are typically between 71 and 317 amino acids in length.
RHEX-like (RHEX-like)
Type: Family

Human RHEX regulates erythroid progenitor cell expansion and erythroblast development .
Protein of unknown function DUF4693 (DUF4693)
Type: Family

This family of proteins is found in chordates. Proteins in this family are typically between 238 and 436 amino acids in length.
Domain of unknown function DUF5094 (DUF5094)
Type: Domain

This entry represents a domain found in a group of microsporidial-specific proteins with unknown function. However, there may be distant homology to Csm1 (

).
Protein of unknown function DUF4694 (DUF4694)
Type: Family

This uncharacterised family includes human protein TNT or C16orf82.
Protein of unknown function DUF4695 (DUF4695)
Type: Family

This uncharacterised family has a conserved RFKTQP sequence motif.
Putative Mad3/Bub1 like region 1 protein (Mad3_Bub1_I_2)
Type: Family

This family of microsporidial sequences may be related to the Mad3/Bub1 homology region 1 domain (

).