SII-SWORD/CoKE huggingface dataset:
Inclusion membrane protein E (IncE)
Type: Family

The chlamydial inclusion membrane is extensively modified by the insertion of type III secreted effector proteins . These inclusion membrane proteins (Incs) have two major characteristics: an N-terminal type III secretion signal that is necessary for their secretion out of the bacterium and a hydrophobic region consisting of at least two trans-membrane helices that allows insertion into the inclusion membrane. Generally, both the N- and C-terminal regions of the Inc are exposed to the host cell cytosol .

This family has members such as the IncE (also known as CT116) proteins found in Chlamydia trachomatis. IncE Interacts with Retromer-Associated Sorting Nexins (SNXs) directly binding the PX-domains of SNX5/6. It is expressed within the first 2 hours of C. trachomatis infection. IncE region 101-132 is the binding site for SNX5/6 causing re-localization of SNX5/6 from endosomes to the inclusion membrane. IncE101-132 expression was shown to be sufficient to maintain CI-MPR (Cation-Independent Mannose-6-Phosphate Receptor) in retromer-containing compartments, thereby disrupting efficient CI-MPR trafficking to the trans-Golgi. It has been suggested that SNX5/6 bind directly to IncE independently of phosphoinositides and that the predicted IncE C-terminal β-hairpin is required. IncE-mediated sequestration of retromer SNX-BAR proteins may promote Golgi fragmentation, a process that facilitates lipid acquisition by C. trachomatis and enhances progeny production .
Inclusion membrane protein F (IncF)
Type: Family

The chlamydial inclusion membrane is extensively modified by the insertion of type III secreted effector proteins. These inclusion membrane proteins (Incs) are exposed to the cytosol and share a common structural feature of a long, bi-lobed hydrophobic domain but little or no primary amino acid sequence similarity .

This family has members such as the IncF proteins found in Chlamydia trachomatis. IncF is enriched at the point of contact of RBs (reticulate bodies) with the inclusion membrane . It is expressed early in the developmental cycle and interacts with many other Inc proteins, like Ct058 or Ct850, which are expressed later during the cycle. Thus, IncF could act as an interaction node for Inc proteins. IncF consists of 104 amino acids of which 38 N-terminal amino acids encoding the signal sequence for the type III system and 12 C-terminal amino acids may be localized in the host cell cytoplasm. Suggesting that IncF or other small Incs interact with other Inc proteins by their trans-membrane domain. It has been identified to be capable of homo-oligomerization and also displayed self-interacting properties .
Protein of unknown function DUF5509 (DUF5509)
Type: Family

This is a family of unknown function found in Baculoviridae.
Uncharacterized protein US30-like (US30-like)
Type: Family

This is a family of unknown function found in Cytomegalovirus. One of the family members US30 is a putative membrane glycoprotein with one predicted trans-membrane region. This entry also includes Uncharacterized protein HHRF5.
Uncharacterized protein B277 (B277)
Type: Family

This is a family of unknown function, however family members such as B277 have been suggested to play a role in viral function .
Viral unique long protein 16 (UL16)
Type: Family

This family contains members such as UL16 found in the human cytomegalovirus (HCMV). It is an immunoevasin which subverts NKG2D-mediated immune responses by retaining a select group of diverse NKG2D ligands inside the cell. UL16 is a heavily glycosylated 50kDa type I trans-membrane glycoprotein. The ectodomain folds into a modified version of the a variable (V-type) (immunoglobulin Ig)-like domain. The N-terminal 'plug' region (amino acids 27-50) is covalently linked to the Ig-like core with a disulfide bond. UL16 protein utilizes a three-stranded β-sheet to engage the α-helical surface of the MHC class I-like MICB platform domain. Residues at the centre of this β-sheet mimic a central binding motif employed by the structurally unrelated C-type lectin-like NKG2D to facilitate engagement of diverse NKG2D ligands .
Protein of unknown function DUF5508 (DUF5508)
Type: Family

This is a family of unknown function found in Enterobacteriaceae. It includes uncharacterised protein YpjB.
Protein ORF45 (ORF45)
Type: Family

Family members found in alphabaculoviruses such as orf45 have been implicated in late gene expression when linked to orf41 .
Secreted clade V protein (SCVP)
Type: Family

Family members are found in strongylid parasites (A. ceylanicum, N. americanus, H. contortus and Heterorhabditis bacteriophora) and in related non-parasitic clade V species (C. elegans, Caenorhabditis briggsae and P. pacificus), hence the name secreted clade V proteins (SCVPs). In Ancylostoma ceylanicum, the encoded 150 residue proteins are predicted to be classically secreted .
Strongylid L4 protein-like (SL4P)
Type: Family

Family members are predicted non-classically secreted proteins found in Ancylostoma ceylaniucum. Homologs are found in strongylids A. ceylanicum, N. americanus, H. contortus and Angiostrongylus cantonensis, where the corresponding genes in A. cantonensis are expressed in L4 larvae. Thus this family members found in A. ceylaniucum have been named strongylid L4 proteins (SL4Ps). Although SL4Ps do not resemble any domains of known function, they do have a conspicuous number of charged residues (both acidic and basic) in their N-terminal, most highly conserved regions .
Viral unique short region 10 (US10)
Type: Family

This family contains US10 proteins found in Human cytomegalovirus (HCMV). US10 is a unique short region trans-membrane glycoprotein found in the endoplasmic reticulum (ER). It down-regulates cell surface expression of HLA-G, but not that of classical class I MHC molecules. Despite of binding to classical class I MHC molecules and delaying their trafficking, it does not affect their steady-state cell surface levels. US10 contains a tri-leucine motif in the cytoplasmic tail which is responsible for down-regulation of HLA-G .
Viral unique short region 6 (US6)
Type: Family

This family has members such as US6 (

) found in HCMV (Human cytomegalovirus). US6 is a unique short region glycoprotein found in the ER. It blocks the binding of ATP by TAP1 (Transporter associated with Antigen Processing 1) through a conformational change and subsequently inhibits TAP-mediated peptide translocation to the ER. It also down regulates MHC class I . Inhibition of US6 of TAP has been shown to require residues 89 to 108 of the HCMV US6 luminal domain, whereas sequences that flank this region stabilize the binding of the viral protein to TAP. Residues 81 to 90 and the C-terminal 39 residues of HCMV US6 may also contribute to the stabilization of the interaction between US6 and TAP .
Protein of unknown function DUF5502 (DUF5502)
Type: Family

This is a family of unknown function found in Listeria.
Protein of unknown function DUF5501 (DUF5501)
Type: Family

This is a family of unknown function found in Alphabaculovirus.
Protein of unknown function DUF5499 (DUF5499)
Type: Family

This is a family of unknown function found in Myoviridae.
Protein of unknown function DUF5498 (DUF5498)
Type: Family

This is a family of unknown function found in Myoviridae.
Protein of unknown function DUF5496 (DUF5496)
Type: Family

This is a family of unknown function found in Myoviridae.
Protein of unknown function DUF5486 (DUF5486)
Type: Family

This is a family of unknown function found in Myoviridae.
Discriminator of mRNA degradation (Dmd)
Type: Family

This family includes Dmd peptides from T4 phages. Dmd can suppress the toxicities of toxins such as LsoA (an endoribonucleases toxin expressed by E.coli). Crystal structure analysis show that Dmd is inserted into the deep groove between the N-terminal repeated domain (NRD) and the Dmd-binding domain (DBD) of LsoA. Site-directed mutagenesis of Dmd revealed the conserved residues (W31 and N40) are necessary for LsoA binding and the toxicity suppression .
Protein of unknown function DUF5485 (DUF5485)
Type: Family

This is a family of unknown function found in Alphabaculovirus.
Bacillus competence protein S (ComS)
Type: Family

ComS, a protein 46 amino acids in length, is described as the product of a gene fully embedded in the much longer gene srfAB, which encodes a non-ribosomal peptide synthetase subunit involved in surfactin biosynthesis. The gene is encoded on the same strand, allowing ComS to be produced from the same mRNA as SrfAB. ComS is seen as crucial for competence development as it prevents proteolytic degradation of ComK, the key transcriptional activator of all genes required for the uptake and integration of DNA .
Protein of unknown function DUF5484 (DUF5484)
Type: Family

This family of unknown function is mainly found in Myoviridae.
Cytomegalovirus UL20 (UL20)
Type: Family

This family has members such as the human cytomegalovirus glycoprotein UL20. UL20 is a type I trans-membrane glycoprotein with an immunoglobulin-like ectodomain that is highly polymorphic among HCMV strains .
Protein of unknown function DUF5483 (DUF5483)
Type: Family

This is a family of unknown function found in Saccharomycetales.
Proteasome subunit alpha 1 (Proteasome_alpha1)
Type: Family

This entry represents the constitutive proteasome subunit alpha 1 , also known as Prosalpha6 (in
Drosophila melanogaster
) and Pre5 or alpha 6 (in fungi) . This subunit is replaced in the
D. melanogaster
spermatoproteasome .

The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated α-β-β-α cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis . Mammals have 7 alpha and 7 beta proteasome subunits while archaea have one of each.
Protein of unknown function DUF5482 (DUF5482)
Type: Family

This is a family of unknown function mainly found in Saccharomycetales.
Protein of unknown function DUF5481 (DUF5481)
Type: Family

This is a family of unknown function found in Myoviridae.
ECORI-T site protein ETM (ETM)
Type: Family

This is a family of unknown function found in Alphabaculovirus .
Protein of unknown function DUF5480 (DUF5480)
Type: Family

This is a family of proteins of unknown function found in phages.
Protein of unknown function DUF5479 (DUF5479)
Type: Family

This is a family of unknown function found in Kappa-papillomavirus.
Inhibitor of toxin/antitoxin system (TA_inhibitor)
Type: Family

This is a family of prokaryotic toxin-antitoxin (TA) systems inhibitors, found in Podoviridae such as Enterobacteria phage T7. Family members such as Gene product 4.5 have been shown to neutralize TA-system-mediated abortive infection by inhibiting the Lon protease activity, thus preventing antitoxin degradation and toxin activation .
GA-like domain (GA-like)
Type: Domain

This domain is found in bacterial cell surface proteins. It is related to the GA domain that forms a three helix bundle (

).
Protein of unknown function DUF5473 (DUF5473)
Type: Family

This is a family of unknown function found mainly in Human mastadenovirus.
Protein of unknown function DUF5472 (DUF5472)
Type: Family

This is a family of unknown function found in Human papillomavirus.
Protein of unknown function DUF5393 (DUF5393)
Type: Family

This is a family of unknown function found in Trypanosomatidae.
Protein of unknown function DUF5471 (DUF5471)
Type: Family

This is a family of unknown function found in Enterobacteria phage T7.
Protein of unknown function DUF5395 (DUF5395)
Type: Family

This is a family of unknown function found in Archaea and Bacteria.
Protein of unknown function DUF5396 (DUF5396)
Type: Family

This is a family of unknown function found in Mycoplasma.
Protein of unknown function DUF5334 (DUF5334)
Type: Family

This is a family of unknown function found mainly in Proteobacteria.
Protein of unknown function DUF5332 (DUF5332)
Type: Family

This family of proteins is mostly found in Chromadorea. Proteins in this family include dct-5. Dct-5 is a target of DAF-16, a forkhead transcription factor, which is a key regulator of longevity, metabolism and dauer diapause in Caenorhabditis elegans .
Protein of unknown function DUF5470 (DUF5470)
Type: Family

This is a family of unknown function found in viruses.
Protochlamydia outer membrane protein (Pom)
Type: Domain

This domain has been found in an outer membrane protein from environmental chlamydia. It shows porin function .
Cupiennin (Cupiennin)
Type: Family

Cupiennin are small cationic α-helical peptides from the venom of the ctenid spider Cupiennius salei, which are characterised by high bactericidal as well as hemolytic activities . Family members such as cupiennin 1a exert both cytolytic and antibacterial effects. The cytolytic activity of the cupiennin peptides depends primarily on the amphipathic N terminus, which is capable of inserting into the membrane, and is modulated by the C terminus via electrostatic interactions with the cell surface .
Protein of unknown function DUF5319 (DUF5319)
Type: Family

This is a family of unknown function mostly found in Actinobacteria.
Protein of unknown function DUF5336 (DUF5336)
Type: Family

This Actinobacterial family of proteins has no known function. Most of the family members are predicted to have have 4 trans-membrane regions.
Protein of unknown function DUF5316 (DUF5316)
Type: Family

This is a family of unknown function mainly found in Firmicutes. It might contain multiple trans-membrane sequences.
Protein of unknown function DUF5317 (DUF5317)
Type: Family

This is a family of unknown function found mainly in Bacteria. Members of this family have multiple trans-membrane domains with the majority typically constituted of 4 trans-membrane regions.
Protein of unknown function DUF5318 (DUF5318)
Type: Family

This family of unknown function is mostly found in Actinobacteria.
Metastasis-associated protein MTA1, R1 domain (MTA1_R1)
Type: Domain

The R1 domain is found in the MTA1 protein and its homologues. The domain is composed of 4 α helices. It has been shown to bind to the RBBP4 protein . The MTA proteins contain a second partial copy of this domain called R2. The R2 domain is matched by this model for some proteins.
Aphid megourin (Megourin)
Type: Family

This family is found in the vetch aphid Megoura viciae with members such as Megourin 1, 2 and 3. Megourins are antimicrobial peptides that act against Gram-positive bacteria and fungi .
Protein of unknown function DUF5302 (DUF5302)
Type: Family

This is a family of unknown function found in Actinobacteria with highly conserved motif of FRRKSG found at the C terminus.
Sulphur globule protein (SGP)
Type: Family

Sulphur globules are membrane-bounded intracellular globules, used by purple sulphur bacteria to transiently store sulphur during the oxidisation of reduced sulphur compounds . This proteobacterial family contains structural proteins of these sulphur globules, and includes sulphur globule protein CV1 (SgpA) and sulphur globule protein CV2 (SgpB).
Serine/threonine-protein kinase SMG1, N-terminal (SMG1_N)
Type: Domain

This entry represents the N-terminal domain of SMG1, which is a member of the phosphoinositide 3 kinase-like kinase (PIKK) family. SMG1 associates with components of the mRNA surveillance complex and is involved in the regulation of nonsense-mediated mRNA decay . It also plays an important role in genotoxic stress responses to DNA damage .
Elicitor peptide (PEP)
Type: Family

This entry include a group of elicitor peptides from plants, including Arabidopsis AtPEP1-7. AtPEP1 activates transcription of the defensive gene defensin (PDF1.2) and activates the synthesis of H(2)O(2), both being components of the innate immune response . It also induces lignin and callose depositions, which leads to strengthen cell walls in root as part of the immune response .
Type VI secretion system TssN (TssN)
Type: Family

TssN proteins have multiple predicted transmembrane (TM) regions. In Flavobacterium johnsoniae, three specific components (TssN, TssO and TssP) are absent in the other sub-types of T6SS .

The type VI secretion system (T6SS), also known as CIS contractile injection system , is a supra-molecular bacterial complex that resembles phage tails. It is a toxin delivery systems which fires toxins into target cells upon contraction of its TssBC sheath . Thirteen essential core proteins are conserved in all T6SSs: the membrane associated complex TssJ-TssL-TssM, the baseplate proteins TssE, TssF, TssG, and TssK, the bacteriophage-related puncturing complex composed of the tube (Hcp), the tip/puncturing device VgrG, and the contractile sheath structure (TssB and TssC). Finally, the starfish-shaped dodecameric protein, TssA, limits contractile sheath polymerization at its distal part when TagA captures TssA .
Protein of unknown function DUF5466 (DUF5466)
Type: Family

This is a family of unknown function mainly found in Enterobacteria phage T7.
Protein of unknown function DUF5314 (DUF5314)
Type: Family

This is a family of fungal proteins that includes a variety of retrotransposons.
Protein of unknown function DUF5464 (DUF5464)
Type: Family

This is a family of unknown function found in Bacteriophages.
Protein of unknown function DUF5463 (DUF5463)
Type: Family

This is a family of unknown function found in Yersinia.
Protein of unknown function PsaF (PsaF)
Type: Family

This is a family of unknown function mainly found in Yersinia.
Protein of unknown function DUF5304 (DUF5304)
Type: Family

This family of unknown function is found in Actinobacteria.
DNA replication protein 17 (Phage_Gp17)
Type: Family

Protein 17 (gene product 17/gp17), found in Bacillus phage phi29, is involved in DNA replication and in pulling the phage DNA into the cell during the injection process .
Protein of unknown function DUF5305 (DUF5305)
Type: Family

This family consists of several hypothetical proteins of unknown function.
Protein of unknown function DUF5308 (DUF5308)
Type: Family

This family of uncharacterised fungal proteins are primarily found in ascomycota.
Mitochondrial peculiar membrane protein 1 (Mpm1)
Type: Family

This family contains mitochondrial peculiar membrane proteins, found predominantly in Saccharomycetales. Proteins in this entry include Mpm1 from S. cerevisiae .
Histone-like protein p6 (Histone-like_p6)
Type: Family

Family members such as protein p6 from Bacillus subtilis phage phi29 bind double-stranded DNA, forming a large nucleoprotein complex all along the viral genome, and have been proposed to be an architectural protein with a global role in genome organization. P6 is also involved in viral transcriptional control, repressing the C2 early promoter located at the right DNA end, and together with the viral regulatory protein p4, repressing early promoters A2b/A2c and activating late promoter A3 .
Std1/Mth1 (Std1/Mth1)
Type: Family

This family of proteins includes the known homologues Std1 (also known as MSN3) and Mth1. Both Std1 and Mth1 are involved in modulating the expression of glucose-regulated genes in yeast, but have been shown to function by slightly different methods. It has been suggested that both Std1 and Mth1 are required to repress the hexose transporter genes in low glucose conditions . Std1 has also been shown to stimulate Snf1 kinase through interaction with the catalytic domain of Snf1, antagonising auto-inhibition and promoting an active conformation of the kinase .
K88 minor fimbrial subunit FaeF (FaeF)
Type: Family

FaeF is a K88 minor fimbrial subunit that plays an essential role in the biogenesis of the K88 fimbriae .
NUP160, helical domain, plants (NUP160_hel_plant)
Type: Domain

This entry represents an helical domain found in the central region of NUP160 from Arabidopsis, also known as SAR1 . NUP160 is required for nuclear mRNA export and for disease resistance and for proper expression of factors responsible for the repression of auxin signalling . Together with SAR3, it is essential for ensuring proper chromatin condensation and meiotic repair of double-strand breaks (DSBs) . Moreover, NUP160 is required for anchoring HOS1 (HIGH EXPRESSION OF OSMOTICALLY RESPONSIVE GENES 1) to the nuclear pore complex (NPC), an integrator to mount adequate stress responses. NUP160 and HOS1 may act in concert to promote tolerance to low-energy stress via the SnRK1 kinase .
Beta defensin 50 (Defb50)
Type: Family

B-defensin are small cationic antimicrobial peptides. Beta-defensin 50 (Defb50) has poor antimicrobial activity in its oxidised form, but this improves under reduced conditions .
Protein of unknown function DUF5461 (DUF5461)
Type: Family

This is a family of unknown function found in Sulfolobus viruses.
ERMES regulator 1 (Emr1)
Type: Family

The endoplasmic reticulum-mitochondria encounter structure (ERMES) complex creates contact sites between the endoplasmic reticulum and mitochondria, playing crucial roles in interorganelle communication, mitochondrial fission, mtDNA inheritance, lipid transfer, and autophagy. Emr1, also known as Mco6 in budding yeasts, mediates the formation ERMES foci, thereby contributing to the formation of ER-mitochondrial contact sites .
Protein of unknown function DUF5312 (DUF5312)
Type: Family

This is a family of unknown function, mostly found in Spirochaetia.
Protein of unknown function DUF5313 (DUF5313)
Type: Family

This is a family of unknown function, found mostly in Actinobacteria and composed of trans-membrane proteins.
SU10 major capsid protein (SU10_MCP)
Type: Family

This family (previously known as DUF5309) represents the bacteriophage SU10 major capsid protein and related proteins found in phages and bacteriophages. The capsid of SU10 is organised in fivefold symmetry and build from 715 copies of major capsid protein . The major capsid protein of SU10 adopts an HK97 fold, which is common among tailed bacteriophages and herpesviruses . This protein forms capsomers of two types: pentamers and hexamers.
Cell division control protein 24, OB domain 2 (Cdc24_OB2)
Type: Domain

This entry represents the second OB-fold domain found in cell division control protein 24 (Cdc24).

The OB-fold domains are nucleic acid binding domains. Cdc24 plays an essential role in the progression of normal DNA replication and is required to maintain genomic integrity . Cdc24 has been reported to interact with replication factor C (RFC) as well as proliferating cell nuclear antigen (PCNA), and has been suggested to act as a target for the regulation of damage repair DNA synthesis .
Cell division control protein 24, OB domain 1 (Cdc24_OB1)
Type: Domain

This entry represents the first OB-fold domain found in cell division control protein 24 (Cdc24).

The OB-fold domains are nucleic acid binding domains. Cdc24 plays an essential role in the progression of normal DNA replication and is required to maintain genomic integrity . Cdc24 has been reported to interact with replication factor C (RFC) as well as proliferating cell nuclear antigen (PCNA), and has been suggested to act as a target for the regulation of damage repair DNA synthesis .
Cell division control protein 24, OB domain 3 (Cdc24_OB3)
Type: Domain

This entry represents the third OB-fold domain found in cell division control protein 24 (Cdc24).

The OB-fold domains are nucleic acid binding domains. Cdc24 plays an essential role in the progression of normal DNA replication and is required to maintain genomic integrity . Cdc24 has been reported to interact with replication factor C (RFC) as well as proliferating cell nuclear antigen (PCNA), and has been suggested to act as a target for the regulation of damage repair DNA synthesis .
NADH-ubiquinone oxidoreductase 11kDa subunit (NDUFB11)
Type: Family

Complex I of the respiratory chain is a proton-pumping NADH ubiquinone oxidoreductase that oxidises NADH in the electron transport pathway. Plants contain the series of 14 highly conserved complex I subunits found in other eukaryotic and related prokaryotic enzymes .