SII-SWORD/CoKE huggingface dataset:
Putative Actinobacterial Holin-X, holin superfamily III (Phage_holin_3_6)
Type: Family

Phage_holin_3_6 is a family of small hydrophobic proteins with two or three transmembrane domains of the Hol-X family. Holin proteins are produced by double-stranded DNA bacteriophages that use an endolysin-holin strategy to achieve lysis of their hosts. The endolysins are peptidoglycan-degrading enzymes that are usually accumulated in the cytosol until access to the cell wall substrate is provided by the holin membrane lesion.
Nmi/IFP 35 domain, N-terminal (Nmi/IFP35_N)
Type: Domain

This entry represents the N terminus of interferon-induced 35kDa protein (IFP 35) (approximately 80 residues long), which contains a leucine zipper motif in an α helical configuration . This group of proteins also includes N-myc-interactor (Nmi), a homologous interferon-induced protein.
Fungal chitosanase (Chitosanase_fungal)
Type: Family

This family consists of chitosanase proteins. Chitin, xylan, 6-O-sulphated chitosan and O-carboxymethyl chitin are indigestible by chitosanase .
Protein of unknown function DUF1473 (DUF1473)
Type: Family

This entry represents a family of hypothetical proteins of around 150 residues in length found in Borrelia species. The function of this family is unknown.
TscT toxin domain (DUF1474)
Type: Domain

This entry represents a domain of unknown function in bacterial proteins of around 100 residues in length. These proteins seem to be found exclusively in Staphylococcus species. The function of these proteins is unknown. This entry includes TscT protein , which is part of the TscT/TscA toxin-antitoxin system, also named DUF1474 family protein.
Protein of unknown function DUF1475 (DUF1475)
Type: Family

This family consists of several hypothetical plant proteins of around 250 residues in length. The function of this family is unknown.
Amastin surface glycoprotein (Amastin)
Type: Family

This family contains the eukaryotic surface glycoprotein amastin (approximately 180 residues long).In Trypanosoma cruzi, amastin is particularly abundant during the amastigote stage .
ATPase inhibitor subunit zeta (ATPase_inh_sub_z)
Type: Family

This entry represents zeta-subunits, which are found in alpha-proteobacterial F1F0-ATPase regulatory proteins. The zeta subunit is a potent inhibitor of the alpha-proteobacterial F1FO-ATPase. The inhibitory region resides in the first 14 N-terminal residues of the protein, which protrude from the 4-α-helix bundle structure of the isolated zeta subunit .
Autographa californica nuclear polyhedrosis virus, Orf4 (AcMNPV_Orf4)
Type: Family

This entry is represented by Orf4 in EGT-IAP1 intergenic region fom Autographa californica nuclear polyhedrosis virus (AcMNPV), also known as Uncharacterized 12.2 kDa protein. It is a family of uncharacterised viral proteins.
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7 (NDUA7)
Type: Family

This family contains the eukaryotic NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7 (NDUA7 or NDUFA7, also known as NADH:ubiquinone oxidoreductase subunit B14.5a, Complex I-B14.5a). This is approximately 100 residues long, and forms part of a multiprotein complex that resides on the inner mitochondrial membrane and it is part of the accessory subunits, not involved in catalysis .
Syd (Syd)
Type: Family

This family contains the Syd protein that has been implicated in the Sec-dependent transport of polypeptides across the inner membrane in bacteria. Syd has been shown to bind the SecY subunit of membrane-embedded SecYEG heterotrimer (also known as core translocon or SecY complex) which is a conserved protein-conducting channel essential for the biogenesis of most of the secretory and integral membrane proteins . The SecY-binding site of Syd is a conserved concave and electronegative groove that forms interactions with the electropositive loops of the SecY subunit . Syd is also known to verify the proper assembly of the SecY complex in the membrane by interfering with protein translocation only when the channel displays abnormal SecY-SecE associations .
Sapovirus VP3 (Sapovirus_VP3)
Type: Family

This family consists of several hypothetical Sapovirus VP3 proteins of around 165 residues in length. The function of this family is unknown.
Protein of unknown function DUF1480 (DUF1480)
Type: Family

This family consists of several hypothetical Enterobacterial proteins of around 80 residues in length. The function of this family is unknown.
Host-nuclease inhibitor protein Gam (Host-nuc_inhib_Gam)
Type: Family

The Gam protein, originally characterised in Bacteriophage Mu, protects linear double stranded DNA from exonuclease degradation
in vitro
and
in vivo
. This protein is also found in many bacterial species as part of a suspected prophage. Further studies have shown that Gam is a functional counterpart of the eukaryotic Ku protein, which has key roles in DNA repair and in certain transposition events.
Gam displays DNA binding characteristics remarkably similar to those of human Ku . In addition, Gam can interfere with Ty1 retrotransposition in Saccharomyces cerevisiae (Baker's yeast). These data reveal structural and functional parallels between bacteriophage Gam and eukaryotic Ku and suggest that their functions have been evolutionarily conserved .
Uroplakin-2 (Uroplakin-2)
Type: Family

This family contains Uroplakin-2, which is approximately 180 residues long and seems to be restricted to mammals. Uroplakin II is an integral membrane protein, and is one of the components of the apical plaques of mammalian urothelium formed by the asymmetric unit membrane - this is believed to play a role in strengthening the urothelial apical surface to prevent the cells from rupturing during bladder distension .

Uroplakins (UPs) are a family of proteins that associate with each other to form plaques on the apical surface of the urothelium, the pseudo-stratified epithelium lining the urinary tract from renal pelvis to the bladder outlet . UPs are classified into 3 types: UPIa and UPIb, UPII, and UPIIIa and IIIb. UPIs are tetraspanins that have four transmembrane domains separating one large and one small extracellular domain while UPII and UPIIIs are single-pass transmembrane proteins. UPIa and UPIb form specific heterodimers with UPII and UPIII, respectively, which allows them to exit the endoplasmatic rediculum. UPII/UPIa and UPIIIs/UPIb form heterotetramers and six of these tetramers form the 16nm particle, seen in the hexagonal array of the asymmetric unit membrane, which is believed to form a urinary tract barrier . Uroplakins are also believed to play a role during urinary tract morphogenesis .
Dinitrogenase reductase ADP-ribosyltransferase (DRA_trans)
Type: Family

This family consists of several bacterial dinitrogenase reductase ADP-ribosyltransferase (DRAT) proteins. Members of this family seem to be specific to Rhodospirillum, Rhodobacter and Azospirillum species. Dinitrogenase reductase ADP-ribosyl transferase (DRAT) carries out the transfer of the ADP-ribose from NAD to the Arg-101 residue of one subunit of the dinitrogenase reductase homodimer, resulting in inactivation of that enzyme. Dinitrogenase reductase-activating glycohydrolase (DRAG) removes the ADP-ribose group attached to dinitrogenase reductase, thus restoring nitrogenase activity. The DRAT-DRAG system negatively regulates nitrogenase activity in response to exogenous NH4+ or energy limitation in the form of a shift to darkness or to anaerobic conditions .
Protein of unknown function DUF1482 (DUF1482)
Type: Family

This family consists of several Enterobacterial proteins of around 60 residues in length. The function of this family is unknown.
Liver-expressed antimicrobial peptide 2 (LEAP-2)
Type: Family

This family consists of several mammalian liver-expressed antimicrobial peptide 2 (LEAP-2) sequences. LEAP-2 is a cysteine-rich, and cationic protein. LEAP-2 contains a core structure with two disulphide bonds formed by cysteine residues in relative 1-3 and 2-4 positions. LEAP-2 is synthesised as a 77-residue precursor, which is predominantly expressed in the liver and highly conserved among mammals. The largest native LEAP-2 form of 40 amino acid residues is generated from the precursor at a putative cleavage site for a furin-like endoprotease. In contrast to smaller LEAP-2 variants, this peptide exhibits dose-dependent antimicrobial activity against selected microbial model organisms . The exact function of this family is unclear.
Post-segregation antitoxin CcdA (Post-segregation_anti-tox_CcdA)
Type: Family

This entry consists of several Enterobacterial post-segregation antitoxin CcdA proteins. The F plasmid-carried bacterial toxin, the CcdB protein, is known to act on DNA gyrase in two different ways. CcdB poisons the gyrase-DNA complex, blocking the passage of polymerases and leading to double-strand breakage of the DNA. Alternatively, in cells that overexpress CcdB, the A subunit of DNA gyrase (GyrA) has been found as an inactive complex with CcdB. Both poisoning and inactivation can be prevented and reversed in the presence of the F plasmid-encoded antidote, the CcdA protein .
Protein of unknown function DUF1484 (DUF1484)
Type: Family

This family consists of several hypothetical bacterial proteins of around 110 residues in length. Members of this family appear to be found in Ralstonia solanacearum and related betaproteobacteria. The function of this family is unknown.
Conotoxin, alpha-type (Conotoxin_a-typ)
Type: Family

This family consists of several alpha conotoxin precursor proteins from a number of Conus species. Cone snail toxins, conotoxins, are small peptides with disulphide connectivity, that target ion-channels or G-protein coupled receptors. Based on the number and pattern of disulphide bonds and biological activities, conotoxins can be classified into several families . Alpha-conotoxins are neurotoxins from the venom of fish-hunting cone snails that block nicotinic acetylcholine receptors (nAChRs) . Alpha-conotoxin-like Lv1.4 has analgesic effects in mouse being a potential drug for therapeutic applications . Omega, delta and kappa families of conotoxins have a knottin or inhibitor cystine knot scaffold. The knottin scaffold is a very special disulphide through disulphide knot, in which the III-VI disulphide bond crosses the macrocycle formed by two other disulphide bonds (I-IV and II-V) and the interconnecting backbone segments, where I-VI indicates the six cysteine residues starting from the N terminus.
Polyketide cyclase SnoaL-like (Cyclase_SnoaL-like)
Type: Family

Polyketides form a diverse group of compounds produced mainly by microorganisms and plants. This family of polyketide synthases includes aklanonic acid methyl ester cyclases, involved in the synthesis of aklavinone, an intermediate in the biosynthetic pathway of clinically important anthracyclines such as daunorubicin and doxorubicin . SnoaL belongs to this family; it is involved in nogalamycin biosynthesis .

SnoaL adopts a distorted α-β barrel fold . Structural data together with site-directed mutagenesis experiments have shown that SnoaL has a different mechanism to that of the classical aldolase for catalysing intramolecular aldol condensation .
Fungal fruit body lectin (Fruit_body_lectin_fun)
Type: Family

This family consists of several fungal fruit body lectin proteins. Fruit body lectins are thought to have insecticidal activity and may also function in capturing nematodes . One member of this family, the lectin XCL from Xerocomus chrysenteron, induces drastic changes in the actin cytoskeleton after sugar binding at the cell surface and internalization, and has potent insecticidal activity. The fold of lectin xcl is not related to any of several lectin folds, but but shows significant structural similarity to cytolysins .
Protein of unknown function DUF1487 (DUF1487)
Type: Family

This family consists of several uncharacterised proteins from Drosophila melanogaster. The function of this family is unknown.
Protein of unknown function DUF1488 (DUF1488)
Type: Family

This family consists of several hypothetical bacterial proteins of around 85 residues in length. The function of this family is unknown.
Protein of unknown function DUF1490 (DUF1490)
Type: Family

DUF1490 consists of several hypothetical bacterial proteins of around 90 residues in length. The function of this family is unknown.
Protein of unknown function DUF1491 (DUF1491)
Type: Family

This family consists of several bacterial proteins of around 115 residues in length. Members of this family seem to be found exclusively in the alphaproteobacteria. The function of this family is unknown.
Prosystemin/Systemin (Prosystemin/Systemin)
Type: Family

This family consists of several plant specific Systemin and Prosystemin proteins. Systemin is processed from a larger prohormone protein, called prosystemin, by proteolytic cleavages . Systemin activates a lipid-based signal transduction pathway in which linolenic acid is converted to jasmonic acid, a potent activator of defense gene transcription, including proteinase inhibitor .
Flagellum biosynthesis repressor FlbT (Flagellum_FlbT)
Type: Family

This family consists of several FlbT proteins. FlbT is a post-transcriptional repressor function in flagellum biogenesis. FlbT is associated with the 5' untranslated region (UTR) of fljK (25kDa flagellin) mRNA and that this association requires a predicted loop structure in the transcript. Mutations within this loop abolish FlbT association and result in increased mRNA stability. It is therefore thought that FlbT promotes the degradation of flagellin mRNA by associating with the 5' UTR .
Protein of unknown function DUF1494 (DUF1494)
Type: Family

This family consists of several bacterial proteins of around 175 residues in length. Members of this family seem to be found exclusively in Chlamydia species. The function of this family is unknown.
Pneumovirus M2-2 (Pneumo_M2-2)
Type: Family

This family consists of several Pneumovirus M2-2 proteins. The M2-2 protein acts as a regulatory factor that mediates the switch from transcription to RNA replication . It acts late in infection in which it inhibits viral transcription and up-regulates RNA replication , mediated by phosphorylation of the P protein .
Histone H1-like nucleoprotein HC2 (HC2)
Type: Family

This family contains the bacterial histone H1-like nucleoprotein HC2 (approximately 200 residues long), which seems to be found mostly in Chlamydia. HC2 functions in DNA condensation, although it has been suggested that it also has other roles .
Protein of unknown function DUF1496 (DUF1496)
Type: Family

This family consists of several bacterial proteins of around 90 residues in length. Members of this family seem to be found exclusively in the Orders Vibrionales and Enterobacteriales. The function of this family is unknown.
Protein of unknown function DUF1497 (DUF1497)
Type: Family

This entry represents a family of several short phage and bacterial proteins whose function is not known. This family seems to be found exclusively in Lactococcus lactis and the bacteriophages that infect this organism.
Seadornavirus VP7 (Seadorna_VP7)
Type: Family

This family consists of several Seadornavirus specific VP7 proteins of around 305 residues in length. The function of this family is unknown.
Vaccinia virus, B6 (Vaccinia_virus_B6)
Type: Family

This family consists of several Orthopoxvirus specific proteins, which include Vaccinia virus, B6 protein, also known as Protein OPG191. The function of this family is unknown.
Mycoplasma P30 (P30)
Type: Family

This family consists of several P30 proteins which seem to be specific to Mycoplasma agalactiae. P30 is a 30kDa immunodominant antigen and is known to be a transmembrane protein .
Exocyst complex component Sec10-like (Sec10-like)
Type: Family

This family contains the Sec10 component (approximately 650 residues long) of the eukaryotic exocyst complex, which mediates the tethering of post-Golgi secretory vesicles to the plasma membrane and promotes the assembly of the SNARE complex for membrane fusion . It is also involved in cell polarisation, primary ciliogenesis, cytokinesis, pathogen invasion, tumorigenesis and metastasis. The exocyst is a member of the Complex Associated with Tethering Containing Helical Rods (CATCHRs) which also includes DSL1, COG and GARP complexes, evolutionary related. They share structural features comprising α-helical bundles towards the C-terminal and coiled-coil regions at the N-terminal. It also includes Recyclin-1 and protein Pof6. Recyclin-1 is involved in recycling plasma membrane proteins internalized by endocytosis . Pof6, together with skp1, is essential for septum processing and cell separation .
Mig-14 (Mig-14)
Type: Family

This family contains a number of bacterial mig-14 proteins (approximately 270 residues long). In Salmonella, mig-14 contributes to resistance to antimicrobial peptides, although the mechanism is not fully understood .
Putative Na+/H+ antiporter (Na_H_antiport_3)
Type: Family

This family consists of several hypothetical bacterial proteins of around 440 residues in length. The function of this family is unknown. Many members carry 11 or 12 transmembrane regions, suggesting that they might be transporters. One family member,

is classified by TCDB as being an NhaE type of Na+/H+ antiporter.
Bovine Lentivirus VIF (Lenti_VIF_2)
Type: Family

This family consists of several Lentivirus viral infectivity factor (VIF) proteins. VIF is known to be essential for ability of cell-free virus preparation to infect cells . Members of this family are specific to Bovine immunodeficiency virus (BIV) and Jembrana disease virus (JDV) which also infects cattle.
Human herpesvirus U26 (Herpes_U26)
Type: Family

This family consists of several Human herpesvirus U26 proteins of around 300 residues in length. The function of this family is unknown.
Protein of unknown function DUF1505 (DUF1505)
Type: Family

This family consists of several uncharacterised Caenorhabditis elegans proteins of around 115 resides in length. Members of this family contain 6 highly conserved cysteine residues. The function of this family is unknown.
Seadornavirus VP6 (Seadorna_VP6)
Type: Family

This family consists of several VP6 proteins from the Banna virus as well as a related protein VP5 from the Kadipiro virus. Members of this family are typically of around 420 residues in length. The function of this family is unknown.
Uncharacterised protein family UPF0358 (UPF0358)
Type: Family

This family consists of several hypothetical bacterial proteins of around 90 residues in length. The function of this family is unknown; however they form α-helical bundles and are thought to be involved in control of cell shape .
Crinivirus P26 (Crinivirus_P26)
Type: Family

This family consists of several Crinivirus P26 proteins which seem to be found exclusively in the Lettuce infectious yellows virus. The function of this family is unknown.
Sigma factor-binding transcriptional regulator Crl (Tscrpt_reg_Crl)
Type: Family

This family contains the bacterial Sigma factor-binding protein Crl. This is a transcriptional regulator of the csgA curlin subunit gene for curli fibres that are found on the surface of certain bacteria . These proteins bind to the sigma-S subunit of RNA polymerase, activating expression of sigma-S-regulated genes. It was initially suggested that Crl affects transcription initiation in vitro by other sigmas, such as sigma-70 and sigma-32. However, it is now established that Crl binds specifically to the alternative sigma factor S/RpoS and favors its association with the core RNAP (RNA polymerase), thereby increasing its activity, which in turn regulates general stress response that protects many Gram-negative bacteria from several harmful environmental conditions. Furthermore, sigma S factor/RpoS plays important roles in biofilm formation and virulence of the food-borne pathogen Salmonella enterica serovar Typhimurium .
PilM, inner membrane (IM_PilM)
Type: Family

This entry contains the bacterial protein PilM (approximately 150 residues long). PilM is an inner membrane protein that has been predicted to function as a component of the pilin transport apparatus and thin-pilus basal body .
Domain of unknown function DUF1510 (DUF1510)
Type: Domain

Proteins containing this domain consist of several hypothetical bacterial proteins of around 200 residues in length. Their function is unknown.
TrbM (TrbM)
Type: Family

This family contains the bacterial protein TrbM (approximately 180 residues long). In Comamonas testosteroni T-2, TrbM is derived from the IncP1beta plasmid pTSA, which encodes the widespread genes for p-toluenesulphonate (TSA) degradation . This family also includes MPFK and its functional homologue kikA, which are required for efficient conjugative transfer in IncP-9 plasmids .
Pardaxin (Pardaxin)
Type: Family

This family consists of several Pardaxin proteins. Pardaxin, a 33-amino-acid pore-forming polypeptide toxin isolated from the Red Sea Moses sole Pardachirus marmoratus, has a helix-hinge-helix structure. This is a common structural motif found both in antibacterial peptides that can act selectively on bacterial membranes (e.g., cecropin), and in cytotoxic peptides that can lyse both mammalian and bacterial cells (e.g., melittin). Pardaxin possesses a high antibacterial activity with a significantly reduced haemolytic activity towards human red blood cells compared with melittin . Pardaxin has also been found to have a shark repellent action .
Dynactin subunit 3 (DCTN3)
Type: Family

DCTN3 is the smallest subunit of dynactin, a complex that binds to cytoplasmic dynein and is a required activator for cytoplasmic dynein-mediated vesicular transport. Dynactin localises to the cleavage furrow and to the midbodies of dividing cells, suggesting that it may function in cytokinesis .
Acyltransferase Tri3/Sat12/Sat16/Mac1 (Tri3/Sat12/Sat16/Mac1)
Type: Family

This entry includes Tri3 from Fusarium sporotrichioides , Mac1 from Ustilago maydis , and Sat16/Sat12 from Stachybotrys chartarum . Tri3/Sat12/Sat16 are trichothecene 15-O-acetyltransferases involved in mycotoxins biosynthesis. Mac1 is an acetyltransferase involved in the mannosylerythritol lipids (MELs) biosynthesis .
TDP-N-acetylfucosamine:lipid II N-acetylfucosaminyltransferase (WecF)
Type: Family

TDP-N-acetylfucosamine:lipid II N-acetylfucosaminyltransferase catalyses the synthesis of Fuc4NAc-ManNAcA-GlcNAc-PP-Und (lipid III) as part of the biosynthetic pathway of enterobacterial common antigen (ECA), a polysaccharide comprised of the trisaccharide repeat unit Fuc4NAc-ManNAcA-GlcNAc .
Phloem filament PP1 (PP1)
Type: Domain

This domain represents a conserved region approximately 200 residues long, four copies of which are found within the plant phloem filament protein PP1. This is one of the constituents of the proteinaceous filaments found in the sieve elements of Cucurbita phloem .
Protein of unknown function DUF1512 (DUF1512)
Type: Family

This family consists of several archaeal proteins of around 370 residues in length. The function of this family is unknown.