SII-SWORD/CoKE huggingface dataset:
Cysteine-rich, acidic integral membrane (CRAM_rpt)
Type: Repeat

This entry represents a 24 residue repeated motif from the Trypanosoma brucei cysteine-rich, acidic integral membrane protein precursor (CRAM). CRAM is concentrated in the flagellar pocket, an invagination of the cell surface of the trypanosome where endocytosis has been documented .
Llipid A acylation PagP (LipidA_acyl_PagP)
Type: Family

This family consists of several bacterial lipid A acylation (PagP) proteins. The bacterial outer membrane enzyme PagP transfers a palmitate chain from a phospholipid to lipid A. In a number of pathogenic Gram-negative bacteria, PagP confers resistance to certain cationic antimicrobial peptides produced during the host innate immune response .
Orthopoxvirus C10L (Orthopox_C10L)
Type: Family

This family consists of several Orthopoxvirus C10L proteins. C10L viral protein, also known as OPG024 protein, can play an important role in vaccinia virus evasion of the host immune system. It may consist in the blockade of IL-1 receptors by the C10L protein, a homologue of the IL-1 Ra .
Protein of unknown function DUF1315 (DUF1315)
Type: Family

This family consists of several bacterial proteins of around 90 residues in length. The function of this family is unknown.
Protein of unknown function DUF1317 (DUF1317)
Type: Family

This family consists of several hypothetical bacterial and phage proteins. The function of this family is unknown.
CryBP1 (CryBP1)
Type: Family

This family consists of several CryBP1-like proteins from Bacillus and Paenibacillus species, including Bacillus thuringiensis and Paenibacillus popilliae. Members of this family are thought to be involved in the overall toxicity of the bacteria to their hosts .
Bacteriophage Mu, Gene product J (Phage_Mu_GpJ)
Type: Family

This entry represents the Gene product J from Escherichia phage Mu (GpJ, previously known as Gp36) and similar proteins found in tailed bacteriophages and in bacterial prophages. The structure of GpJ shows a characteristic aromatic hydrophobic core. This protein might interact directly with the Head-tail connector (Gp29) .
Protein of unknown function DUF1322 (DUF1322)
Type: Family

This entry represents a family of hypothetical Borrelia proteins of around 78 residues in length. The function of this family is unknown.
Orthopoxvirus B11R (Orthopox_B11R)
Type: Family

This family consists of several Orthopoxvirus B11R proteins of around 70 residues in length. The function of this family is unknown. B11R is also known as Protein OPG197.
Regulator of MON1-CCZ1 complex, C-terminal (RMC1_C)
Type: Domain

This entry represents the α-helical C terminus (approximately 160 residues) of RMC1, which is a component of the CCZ1-MON1 RAB7A guanine exchange factor (GEF) . This domain serves as a scaffold for CCZ1-MON1 recruitment and bridges the membrane and GEF complex.
Circovirus 2, anti-apoptotic ORF4 (Circovirus2_Orf4)
Type: Family

This family represents the anti-apoptotic ORF4 protein from Circovirus 2, which antagonises host cell apoptosis by interacting with host ferritin heavy chain (FHC). This protein physically binds host FHC, resulting in the reduction of FHC protein levels in host cells. The reduction of FHC concentration further inhibits the accumulation of reactive oxygen in host cells, leading to reduced apoptosis .
Protein of unknown function DUF1326 (DUF1326)
Type: Family

This family consists of several hypothetical bacterial proteins, which seem to be found exclusively in Rhizobium and Ralstonia species. Members of this family are typically around 210 residues in length and contain 5 highly conserved cysteine residues at their N terminus. The function of this family is unknown.
Bacteriophage ES18, Gp24 (Phage_ES18_Gp24)
Type: Family

This entry is represented by Bacteriophage ES18, Gp24. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.

This family consists of several hypothetical bacterial proteins of around 115 residues in length, which seem to be specific to Escherichia coli. The function of this family is unknown.
Protein of unknown function DUF1328 (DUF1328)
Type: Family

This entry represents several hypothetical bacterial proteins of around 50 residues in length. The function of this family is unknown but is thought to be a membrane protein.
Cytoplasmic repetitive antigen-like (CRA_rpt)
Type: Repeat

This entry consists of several repeats of around 42 residues in length. These repeated sequences are found in multiple copies in Trypanosoma cruzi antigens,

contains 23 copies of this repeat . Homologues are also found in Bacillus species, including ribosomal protein L5-like protein.
Circovirus 2, Orf10 (Circovirus2_Orf10)
Type: Family

This family consists of several Circovirus proteins of around 35 residues in length. Members of this family are described as Orf10 proteins and their function is unknown.
Ovarian carcinoma immunoreactive antigen domain (OCIA_dom)
Type: Domain

This domain can be found in several ovarian carcinoma immunoreactive antigen (OCIA) and related eukaryotic sequences. The function of these proteins is unknown .
Pericardin-like repeat (Pericardin-like_rpt)
Type: Repeat

This entry represents a repeated sequence of around 34 residues in length, which is found in multiple copies in Drosophila pericardin and other extracellular matrix proteins .
White spot syndrome virus (WSSV), Orf116/126, C-terminal (WSSV_Orf116/126_C)
Type: Domain

This family represents a conserved region approximately 130 residues long within a number of proteins of unknown function that seem to be specific to the white spot syndrome virus (WSSV).
DNA helicase, TraI type, C-terminal (DNA_helicase_TraI_C)
Type: Domain

This entry represents the C-terminal domain of the bacterial DNA helicase TraI. TraI is a bifunctional protein that catalyses the unwinding of duplex DNA as well as acts as a sequence-specific DNA trans-esterase, providing the site- and strand-specific nick required to initiate DNA transfer . This domain is essential for conjugative DNA transfer .
Microtubule-associated protein 70 (MAP70)
Type: Family

Microtubule-associated protein 70 (MAP70) are plant-specific proteins that interact with microtubules. In Arabidopsis thaliana, there are five MAP70 genes (MAP70-1/2/3/4/5). MAP70-1 associates with MAP70-5 and is essential for the normal banding pattern of secondary cell wall and for the proper development of xylem tracheary elements and wood formation .
Protein ENHANCED DISEASE RESISTANCE 2, C-terminal (EDR2_C)
Type: Domain

This entry represents the C terminus of protein ENHANCED DISEASE RESISTANCE 2 (EDR2) from plants. EDR2 is a negative regulator of the salicylic acid- (SA-) mediated resistance to pathogens, including the biotrophic powdery mildew pathogens Golovinomyces cichoracearum and Blumeria graminis, and the downy mildew pathogen Hyaloperonospora parasitica, probably by limiting the initiation of cell death and the establishment of the hypersensitive response (HR) .
2-oxoadipate dioxygenase/decarboxylase (HGLS)
Type: Family

This entry represents a group of bacterial, fungal and plant sequences, including 2-oxoadipate dioxygenase/decarboxylase (referred to as HGLS and YdcJ) from Escherichia coli. YdcJ, which is involved in D-lysine metabolism, catalyses a successive decarboxylation and intramolecular hydroxylation of 2-oxoadipate forming 2-hydroxyglutarate in a Fe(II) and oxygen-dependent manner. Members of this protein family are thought to belong to the the vicinal oxygen chelate (VOC) superfamily . The structure has been solved (

,

).
RIC1, C-terminal alpha solenoid region (RIC1_C)
Type: Domain

This entry represents the C-terminal α-helical solenoid region of RIC1.

This entry represents RIC1 (Ribosomal control protein1) and has been identified in yeast as a Golgi protein involved in retrograde transport to the cis-Golgi network. It forms a heterodimer with Rgp1 and functions as a guanyl-nucleotide exchange factor which activates YPT6 by exchanging bound GDP for free GTP. RIC1 is thereby required for efficient fusion of endosome-derived vesicles with the Golgi. The RIC1-RGP1 complex participates in the recycling of SNC1, presumably by mediating fusion of endosomal vesicles with the Golgi compartment and may also be indirectly involved in the transcription of both ribosomal protein genes and ribosomal RNA .
Cell division cycle protein 123 (CDC123)
Type: Family

This entry represents the eukaryotic cell division cycle 123 (Cdc123) family, also known as the translation initiation factor eIF2 assembly family. These proteins are approximately 330 residues long. Budding yeast Cdc123 regulates the cell cycle in a nutrient dependent manner . Cdc123 is member of the ATP grasp family that binds the γ subunit of the eukaryotic translation initiation factor 2 (eIF2). eIF2 plays a key role in protein synthesis .
Lactococcus phage 712, M3 (Lactococcus_phage_712_M3)
Type: Family

This family consists of several Lactococcus bacteriophage 712, middle-3 (M3) proteins of around 160 residues in length. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. The function of this family is unknown.
Streptococcus phage 7201, Orf18 (Phage_7201_Orf18)
Type: Family

This family consists of several hypothetical Streptococcus thermophilus bacteriophage proteins of around 235 residues in length. The function of this family is unknown.
Envelope small membrane protein (GP2b)
Type: Family

This entry includes a group of envelope small membrane protein, including GP2b (also known as protein E) from Porcine reproductive and respiratory syndrome virus. It may function as a viroporin in the virion envelope that facilitates uncoating of the virus in order to release the genomic RNA into the cytoplasm for subsequent replication .
Sporulation stage 0, protein M (Spore_0_M)
Type: Family

This family consists of several bacterial SpoOM proteins which are thought to control sporulation in Bacillus subtilis.Spo0M exerts certain negative effects on sporulation and its gene expression is controlled by sigmaH .
Cell division protein ZapD (ZapD)
Type: Family

Cell division protein ZapD enhances FtsZ-ring assembly. It directly interacts with FtsZ and promotes bundling of FtsZ protofilaments, with a reduction in FtsZ GTPase activity .
Modulator of Rho-dependent transcription termination (ROF)
Type: Family

This family consists of several bacterial modulator of Rho-dependent transcription termination (ROF) proteins. ROF binds transcription termination factor Rho and inhibits Rho-dependent termination
in vivo
.
Translocon-associated protein subunit gamma (SSR3)
Type: Family

The translocon-associated protein (TRAP, also known as the signal sequence receptor) complex is required for the efficient translocation of secretory and membrane proteins in the endoplasmic reticulum, and is also involved in the endoplasmic reticulum stress-mediated unfolded protein response pathway. This entry represents the gamma subunit of the translocon-associated proteins. Trap-gamma (also known as SSR3) appears to be required for vascular network formation in murine placental development .
Protein of unknown function DUF1344 (DUF1344)
Type: Family

This family consists of several short, hypothetical bacterial proteins of around 80 residues in length. Members of this family are found in rhizobacteria. The function of this family is unknown.
Protein of unknown function DUF1345 (DUF1345)
Type: Family

This family consists of several hypothetical bacterial proteins of around 230 residues in length. The function of this family is unknown.
UAP56-interacting factor (FYTTD1)
Type: Family

UAP56-interacting factor, also known as UIF, is a mRNA export adaptor that works together with adaptor REF/ALY. It is required for mRNA export from the nucleus to the cytoplasm .
Protein of unknown function DUF1348 (DUF1348)
Type: Family

This family consists of several highly conserved hypothetical proteins of around 150 residues in length. The function of this family is unknown.
Protein of unknown function DUF1349 (DUF1349)
Type: Family

This family consists of several hypothetical bacterial proteins but contains one sequence Ree1 (

) from Saccharomyces cerevisiae . Members of this family are typically around 200 residues in length. The function of this family is unknown.
Lactobacillus prophage Lj928, Orf309 (Prophage_Lj928_Orf309)
Type: Family

This entry is represented by Lactobacillus prophage Lj928, Orf309. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.

This family consists of several bacterial and phage proteins of around 230 residues in length. The function of this family is unknown.
Spot 14 family (Spot_14)
Type: Family

The Spot 14 family includes thyroid hormone-inducible hepatic protein (Spot 14), Mid1-interacting protein and related sequneces. Mainly expressed in tissues that synthesise triglycerides, the mRNA coding for Spot 14 has been shown to be increased in rat liver by insulin, dietary carbohydrates, glucose in hepatocyte culture medium, as well as thyroid hormone. In contrast, dietary fats and polyunsaturated fatty acids, have been shown to decrease the amount of Spot 14 mRNA, while an elevated level of cAMP acts as a dominant negative factor. In addition, liver-specific factors or chromatin organisation of the gene have been shown to contribute to the regulation of its expression . Spot 14 protein is thought to be required for induction of hepatic lipogenesis . Mid1-interacting protein is involved in stabilisation of microtubules .
Protein jagunal (Jagunal)
Type: Family

Protein jagunal is required for endoplasmic reticulum organisation and proper vesicular traffic during Drosophila oogenesis .
GvpD, P-loop domain (GvpD_P-loop)
Type: Domain

This entry represents the N-terminal domain of several archaeal GvpD gas vesicle proteins. This domain includes the P-loop and the basic region 1 (bR1, an arginine-rich region) which are essential for GvpD repressive function .

GvpD is involved in the regulation of gas vesicle formation through the interaction and breakdown induction of the transcriptional activator GvpE .
Transmembrane protein 106 (TMEM106)
Type: Family

This family includes Transmembrane protein 106A/B/C, type II transmembrane proteins which have homology to the late embryogenesis abundant-2 (LEA-2) domain . TMEM106A has been identified as a key factor to regulate macrophage activation and a tumour suppressor in gastric, renal cancer and nonsmall-cell lung carcinoma (NSCLC), being an interesting therapeutic target for the management of NSCLC . TMEM106B localises to late endosomes and lysosomes, and it is involved in dendrite morphogenesis and maintenance by regulating lysosomal trafficking via its interaction with MAP6 . Its overexpression is associated with familial frontotemporal lobar degeneration . It has also been identified as a protein required for productive SARS-CoV-2 infection . Structural analysis of LEA-2 domains revealed that they have a long, conserved lipid-binding groove, implying that TMEM106B and its homologues, Vac7 and Tag1 from yeast, may all be lipid transfer proteins in the lumen of late endocytic organelles.
Protein of unknown function DUF1357 (DUF1357)
Type: Family

This entry represents a family of hypothetical proteins of around 225 residues in length found in Borrelia species. The function of this family is unknown.
Transmembrane protein 242 (TMEM242)
Type: Family

This family consists of several hypothetical eukaryotic proteins of around 125 residues in length. The function of this family is unknown.
Protein of unknown function DUF1361 (DUF1361)
Type: Family

This family consists of several hypothetical bacterial proteins of around 200 residues in length. The function of this family is unknown although some members are annotated as being putative integral membrane proteins.
Anabaena sensory rhodopsin transducer (ASRT)
Type: Family

This entry represents a family of proteins found in bacteria and some archaeal species, including the Anabaena sensory rhodopsin transducer (ASRT) and the hypothetical protein TM1070 from Thermotoga maritima. ASRT, likely to bind sugars or related metabolites, is comprised of a single globular domain with an eight-stranded β-sandwich fold with a well conserved tryptophan at the start of the first strand and a nearly absolutely conserved asparagine located at the end of the second β-strand that is involved in stabilising the characteristic tight turn between strands 2 and 3 of the structure . TM1070 has a β-sandwich structure with a jelly-roll fold.
Protein of unknown function DUF1363 (DUF1363)
Type: Family

This family consists of several Trypanosoma brucei putative variant specific antigen proteins of around 80 residues in length.
Protein of unknown function DUF1366 (DUF1366)
Type: Family

This family consists of several hypothetical Streptococcus bacteriophage proteins of around 130 residues in length. One of the sequences in this family, from phage Sfi11 (

) is known as Gp149. The function of this family is unknown.
Protein of unknown function DUF1367 (DUF1367)
Type: Family

This family consists of several highly conserved, hypothetical bacterial and phage proteins of around 200 resides in length. The function of this family is unknown.
Wound-induced protein Wun1-like (Wun1-like)
Type: Family

This entry consists of several plant wound-induced protein sequences related to WI12 from Mesembryanthemum crystallinum (Common ice plant) (

). Wounding, methyl jasmonate, and pathogen infection is known to induce local WI12 expression. WI12 expression is also thought to be developmentally controlled in the placenta and developing seeds. WI12 preferentially accumulates in the cell wall and it has been suggested that it plays a role in the reinforcement of cell wall composition after wounding and during plant development .
EthD domain (EthD_dom)
Type: Domain

This domain is found in several bacterial and fungal sequences which are related to the EthD (Ethyl tert-butyl ether degradation) protein of Rhodococcus ruber

. In Rhodococcus ruber, EthD is thought to be involved in the degradation of ethyl tert-butyl ether (ETBE) . In Aspergillus terreus, EthD is part of the Pks1 gene cluster that mediates the biosynthesis of an anthraquinone derivative pigment that contributes to conidial pigmentation that provides protection from UV radiation, heat and cold stress .

This domain can be found in some decarboxylases, such as GedI from Aspergillus terreus. GedI is part of the gene cluster that mediates the biosynthesis of geodin, an intermediate in the biosynthesis of other natural products .
Coiled-coil alpha-helical rod protein 1 (HCR)
Type: Family

This entry represents the coiled-coil α-helical rod protein 1 (HCR) from animals. The function of HCR is unknown but it has been implicated in psoriasis in humans and is thought to affect keratinocyte proliferation .
Transmembrane protein 126 (TMEM126)
Type: Family

This entry includes the transmembrane protein 126 A/B (TMEM126A/B) from animals. Human TMEM126B participates in constructing the membrane arm of mitochondrial respiratory complex I .
Protein of unknown function DUF1373 (DUF1373)
Type: Family

This family consists of several hypothetical proteins which seem to be specific to Oryzias latipes (Japanese ricefish). Members of this family are typically around 200 residues in length. The function of this family is unknown.
Sulfolobus islandicus filamentous virus, Orf14 (SIFV_Orf14)
Type: Family

This family consists of several hypothetical Sulfolobus virus proteins of around 100 residues in length. The function of this family is unknown.
Variable length PCR target (Variable_length_PCR_target)
Type: Repeat

This entry represents a 29 residue repeated sequence which seem to be specific to the Ehrlichia chaffeensis variable length PCR target (VLPT) protein. E. chaffeensis is a tick-transmitted rickettsial agent and is responsible for human monocytic ehrlichiosis (HME). The function of this family is unknown .
Photosystem II PsbW, class 2 (PSII_PsbW_class2)
Type: Family

This family represents the low molecular weight transmembrane protein PsbW found in PSII, where it is a subunit of the oxygen-evolving complex. PsbW appears to have several roles, including guiding PSII biogenesis and assembly, stabilising dimeric PSII , and facilitating PSII repair after photo-inhibition . There appears to be two classes of PsbW, class 1 being found predominantly in algae and cyanobacteria, and class 2 being found predominantly in plants. This entry represents class 2 PsbW.

Oxygenic photosynthesis uses two multi-subunit photosystems (I and II) located in the cell membranes of cyanobacteria and in the thylakoid membranes of chloroplasts in plants and algae. Photosystem II (PSII) has a P680 reaction centre containing chlorophyll 'a' that uses light energy to carry out the oxidation (splitting) of water molecules, and to produce ATP via a proton pump. Photosystem I (PSI) has a P700 reaction centre containing chlorophyll that takes the electron and associated hydrogen donated from PSII to reduce NADP+ to NADPH. Both ATP and NADPH are subsequently used in the light-independent reactions to convert carbon dioxide to glucose using the hydrogen atom extracted from water by PSII, releasing oxygen as a by-product .

PSII is a multisubunit protein-pigment complex containing polypeptides both intrinsic and extrinsic to the photosynthetic membrane . Within the core of the complex, the chlorophyll and β-carotene pigments are mainly bound to the antenna proteins CP43 (PsbC) and CP47 (PsbB), which pass the excitation energy on to the reaction centre proteins D1 (Qb, PsbA) and D2 (Qa, PsbD) that bind all the redox-active cofactors involved in the energy conversion process. The PSII oxygen-evolving complex (OEC) oxidises water to provide protons for use by PSI, and consists of OEE1 (PsbO), OEE2 (PsbP) and OEE3 (PsbQ). The remaining subunits in PSII are of low molecular weight (less than 10kDa), and are involved in PSII assembly, stabilisation, dimerisation, and photo-protection .
Phytoreovirus outer capsid P8 (Phytoreo_P8)
Type: Family

This family consists of several Phytoreovirus outer capsid protein P8 sequences .
Protein of unknown function, DUF1378 (DUF1378)
Type: Family

This family consists of hypothetical bacterial and phage proteins of around 59 residues in length. Bacterial members of this family seem to be specific to Enterobacteria. The function of this family is unknown.
Cell division protein ZapC (ZapC)
Type: Family

ZapC (Z-associated protein C) contributes to the efficiency of the cell division process by in maintaining FtsZ ring stability during cell division . It consists of a N-terminal α/β domain which contains a pocket, termed the N-domain pocket, lined with residues important for ZapC function as an FtsZ bundler and a C-terminal domain which contains an additional pocket (C-domain pocket), with a hydrophobic centre surrounded by conserved basic residues, critical for FtsZ binding .
Late nodulin domain (Nodulin_late_dom)
Type: Domain

This entry represents a domain found in a group of plant proteins, including late nodulin sequences which are homologous to the Pisum sativum (Garden pea) ENOD3 protein. ENOD3 is expressed in the late stages of root nodule formation and contains two pairs of cysteine residues toward the proteins C terminus which may be involved in metal-binding .
Protein of unknown function DUF1380 (DUF1380)
Type: Family

This family consists of several hypothetical bacterial proteins of around 140 residues in length. Members of this family seem to be specific to Enterobacteria. The function of this family is unknown.
Protein of unknown function DUF1381 (DUF1381)
Type: Family

This family consists of several hypothetical Staphylococcus and bacteriophage proteins of around 65 residues in length. The function of this family is unknown.
Uncharacterised protein family YebG (Uncharacterised_YebG)
Type: Family

This family consists of several bacterial YebG proteins of around 75 residues in length. The exact function of this protein is unknown but it is thought to be involved in the SOS response. The induction of the yebG gene occurs as cell enter into the stationary growth phase and is dependent on is dependent on cyclic AMP and H-NS .