SII-SWORD/CoKE huggingface dataset:
Probable magnetosome protein Mms48 (Mms48)
Type: Family

Bacterial magnetosomes are intracellular membrane-enclosed, nanosized magnetic crystals. Mms48, along with the three other genes in the same operon, appear to influence magnetosome size and number .
Uncharacterised conserved protein UCP031804 (UCP031804)
Type: Family

There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function. Members of this entry are mainly found in proteobacteria.
Uncharacterised conserved protein UCP031853 (UCP031853)
Type: Family

There is currently no experimental data for members of this group or their homologues. Though they contain a version of the type II restriction endonuclease domain, it lacks the signature P[D]-[D/E]-X-K. It is therefore not clear if members of this group are enzymatically active endonucleases.
Uncharacterised conserved protein UCP031890, Tim44-related (UCP031890_Tim44-rel)
Type: Family

This group consists of bacterial uncharacterised proteins containing a Tim44-like domain (

). Their function is unknown, but a role in transport seems likely.
Uncharacterised conserved protein UCP031982, alpha/beta hydrolase, XabL (UCP031982_abhydr)
Type: Family

This group represents a predicted alpha/beta hydrolase, XabL type.
Uncharacterised conserved protein UCP023238 (UCP023238)
Type: Family

There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function. Members of this entry are mainly found in proteobacteria.
Uncharacterised conserved protein UCP032086 (UCP032086)
Type: Family

There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function. Members of this entry are mainly found in proteobacteria.
ATP synthase protein I, alphaproteobacterial (Atp1_alphaprobac)
Type: Family

Transport ATPases can be lumped into four distinct types, P, F, V, and ABC. The transport ATPase field is paving the way for nanotechnology focused on nano-motors using the F-type ATPases (F(0)F(1)). When these ATPases are driven in reverse by a proton gradient, they have the capacity to interconvert electrochemical energy into mechanical energy and finally into chemical energy, which is conserved in the terminal bond of ATP . This group represents a F-type ATP synthase, subunit I.
Uncharacterised conserved protein UCP032162, transmembrane (UCP032162_TM)
Type: Family

There is currently no experimental data for members of this group of proteins or their homologues, nor do they exhibit features indicative of any function. However, they are predicted to be integral membrane proteins.
Protein of unknown function UCP032178 (UCP032178)
Type: Family

There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function. However, they may be membrane-anchored (based on transmembrane segment prediction).
Uncharacterised conserved protein UCP032209 (UCP032209)
Type: Family

There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function. Members of this entry are mainly found in proteobacteria.
Predicted glycerophosphotransferase, SA2157 type (SA2157_glycerophostrnsf)
Type: Family

This group represents a predicted glycerophosphotransferase, SA2157 type.
Uncharacterised conserved protein UCP032370, VraC (UCP032370_VraC)
Type: Family

This group represents an uncharcterised conserved protein, VraC, which is presumed to form a complex with VraA and VraB .
Dimeric dUTPase Dut-like (Dimeric_Dut-like)
Type: Family

This entry represents a family of proteins from tailed bacteriophages and bacterial prophages, including the phage dimeric dUTPase (Dut) from Staphylococcus virus 69 (

). This protein, which interacts with the Staphylococcus aureus pathogenicity island SaPIbov1 Stl repressor from this bacteria, shows a homodimeric assembly in which each monomer consists of seven α-helices . It contains an extremely variable region that plays a role in the regulatory capacity of this enzyme .
Uncharacterised conserved protein UCP032441 (UCP032441)
Type: Family

There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function. Members of this entry are mainly found in proteobacteria.
Uncharacterised conserved protein UCP032442 (UCP032442)
Type: Family

There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function. Members of this entry are mainly found in proteobacteria.
HTH-type transcriptional regulator Rot (Rot)
Type: Family

This group represents the HTH transcriptional regulator Rot. Rot (repressor of toxin) is a member of the Sar family of transcriptional factors of Staphylococcus aureus. It is a global regulator with both positive and negative effects that mediates modulation of several genes involved in virulence .
L-serine kinase SbnI-like (SbnI-like)
Type: Family

This entry represents a family of bacterial proteins which includes L-serine kinase SbnI. SbnI acts as a heme-dependent transcriptional regulator of the sbn locus, which is involved in Staphyloferrin B biosynthesis. SbnI uses ATP to phosphorylate L-serine, producing O-phospho-L-serine and ADP .
Membrane-anchored ubiquitin-fold protein (MUB)
Type: Family

Ubiquitin-fold proteins are an important class of eukaryotic post-translational modifiers . They are generally short proteins (less than 200 amino acids) which contain the core β-grasp fold (also known as the ubiquitin fold) and a C-terminal extension which enables their attachment to other proteins through the terminal carboxyl group. Protein-conjugated ubiquitins have been implicated an a wide variety of cellular process including proteolysis, DNA repair, transcription and autophagy Some ubiquitin-like proteins are not conjugated to proteins, but are instead anchored to the cell membrane by attachment to phospholipids or isoprenes. The functions of these membrane-associated proteins are not generally well understood. In the case of isoprene attachemnet, the prenyl group may also play a role in enhancing protein-protein interactions.

This entry represents a group of membrane-associated ubiquitin-fold proteins found in plants and animals . In Arabidopsis, membrane-anchored ubiquitin-fold (MUB) proteins recruit and dock specific E2s to the plasma membrane. They appear to interact noncovalently with an E2 surface opposite the active site that forms a covalent linkage with Ub . The animal homologues of MUBs, also known as UBL3, have also been identified as ubiquitin-like proteins .
Peptidase S53, physarolisin II, archaeal-type (Pept_S53_physarolisin-II_arc)
Type: Family

This entry contains serine peptidases belonging to the MEROPS peptidase family S53 (sedolisin family, clan SB). The peptidases all derive from archaeal species but are related to physarolisin II, which is cold-adapted serine-carboxyl peptidase, encoded by the php gene in Physarum polycephalum (Slime mold) .
Glycoside hydrolase, family 57, Saci1162, predicted (Glyco_hydro_57_Saci1162_prd)
Type: Family

O-Glycosyl hydrolases (

) are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families . This classification is available on the CAZy (CArbohydrate-Active EnZymes) website.

This group represents a predicted family 57 glycoside hydrolase, Saci_1162 type.
Uncharacterised conserved protein UCP032675 (UCP032675)
Type: Family

There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function. Members of this entry are mainly found in proteobacteria.
Uncharacterised conserved protein UCP032676, PqqC (UCP032676_PqqC)
Type: Family

This group represents an uncharacterised protein with PqqC domain.
Uncharacterised conserved protein UCP032748 (UCP032748)
Type: Family

There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function. Members of this entry are mainly found in proteobacteria.
Uncharacterised conserved protein UCP032756 (UCP032756)
Type: Family

There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function. Members of this entry are mainly found in proteobacteria.
Uncharacterised conserved protein UCP032762 (UCP032762)
Type: Family

This uncharacterised family is found in Archaea, mainly in Sulfolobus species.
UCP032817-like (UCP032817-like)
Type: Family

This group of uncharacterised proteins are predominantly found in Proteobacteria.
Uncharacterised conserved protein UCP032840 (UCP032840)
Type: Family

There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function. Members of this entry are mainly found in proteobacteria.
Uncharacterised conserved protein UCP032862, iron-sulphur-binding domain-type, SSO0018 (UCP032862_Fe-S-type)
Type: Family

This group represents an uncharacterised protein with iron-sulphur binding domain, SSO0018 type.
Uncharacterised conserved protein UCP032888 (UCP032888)
Type: Family

There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function. Members of this entry are mainly found in proteobacteria.
Uncharacterised conserved protein UCP032899, lipoprotein (UCP032899)
Type: Family

This group represents an uncharacterised conserved lipoprotein.
Archaeal Cdc45 (Arc_Cdc45)
Type: Family

A member of this family of archaeal proteins has been characterised. Saci_0177 (

) encodes a protein previously known as RecJ, which has been renamed as Cdc45 based on its relationship to eukaryotic Cdc45 . Cdc45 may form a constitutive complex with GINS. This CG complex associates with the MCM complex at replication origins and during replication fork progression, and stimulates its helicase activity .
Fimbrial-like protein YadC (Fimbrial-like_YadC)
Type: Family

This entry represents an uncharacterised fimbrial protein, YadC type.
Uncharacterised conserved protein UCP033367, VanZ, Bll3170 (UCP033367_VanZ)
Type: Family

This group represents an uncharacterised protein with VanZ domain, Bll3170 type.
Uncharacterised conserved protein UCP033595 (UCP033595)
Type: Family

There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function. Members of this entry are mainly found in proteobacteria.
Uncharacterised conserved protein UCP033622, transglutaminase-like, CPE1922 (UCP033622_transglutaminase)
Type: Family

This group represents an uncharacterised protein with transglutaminase-like domain, CPE1922 type.
Uncharacterised conserved protein UCP033634 (UCP033634)
Type: Family

There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function. Members of this entry are mainly found in proteobacteria.
Predicted DNA replication protein, bacterial (DNA_replication_prd_bac)
Type: Family

This group represents a predicted DNA replication protein in bacteria.
Uncharacterised conserved protein UCP033725 (UCP033725)
Type: Family

There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function. Members of this entry are mainly found in proteobacteria.
Uncharacterised conserved protein UCP033763 (UCP033763)
Type: Family

There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function. Members of this entry are mainly found in proteobacteria.
Uncharacterised conserved protein UCP033860 (UCP033860)
Type: Family

This group represents an uncharacterised conserved protein from Clostridia.
Uncharacterised conserved protein UCP034039 (UCP034039)
Type: Family

This group represents an uncharacterised conserved protein.
Uncharacterised conserved protein UCP034217 (UCP034217)
Type: Family

This entry represents a group of uncharacterised conserved proteins from bacteria.
Cancer-associated antigen RCAS1 (Cancer-assoc_antigen_RCAS1)
Type: Family

Receptor-binding cancer-associated surface antigen (RCAS1) and Estrogen receptor-binding fragment-associated gene 9 (EBAG9) proteins are identical. EBAG9/RCAS1 induces apoptosis and suppresses the growth of several cells such as activated T cells . Defects in EBAG9 may be a cause of breast cancers and adenocarcinomas of the lung as it is present and overexpressed in many patients and the expression correlates with tumor grade, suggesting that it may be involved in cancer immune escape. It may not be a directly tumor-associated antigen, but rather contributes indirectly to the antigenicity of tumor cells. The selective suppression phenomenon of the cytotoxic immune response may be brought about by an increase in sRCAS1 blood serum concentration. Such an increase has been observed during cancer progression. RCAS1 blood serum concentration could be useful in the identification of endometriosis and prostatic cancer .
Inducible mutagenesis protein A (ImuA)
Type: Family

This entry represents inducible mutagenesis protein A (ImuA), believed to be involved in DNA damage tolerance in a number of bacteria. This protein is often encoded in a operon with DnaE2 (a second copy of the catalytic subunit of DNA polymerase III), and ImuB (whose function is not known though it is similar to the Y-family of DNA polymerases), though the genes may also be encoded in separate regions. In Caulobacter crescentus (Caulobacter vibrioides) the imuAB/dnaE2 operon is induced by DNA damage in a RecA-dependent manner and is required for the error-prone processing of DNA lesions . Strains deficient in these genes showed extreme sensitivity to mutagenic agents such as UV or the drug mitC. The function of ImuA is not known but sequence analysis suggests that it contains a P-loop nucleoside triphosphate hydrolase domain.
STM3548-like (STM3548-like)
Type: Family

This entry represents a family of proteins predominantly found in proteobacteria, including STM3548 from Salmonella typhimurium (

). This protein adopts a hexameric configuration. Each monomer shows a globular domain that contains eight α-helices and thirteen β-strands and has a three-layer α/β/α sandwich flavodoxin-like fold, and a hairpin protrusion which occupies a central position in the hexamer. It seems to contain a type 1 glutamine amidotransferase (GATase1)-like domain (

) .
Uncharacterised conserved protein UCP034456 (UCP034456)
Type: Family

This group represent uncharacterised proteins.
Putative phage head morphogenesis protein (Phage_head_put)
Type: Family

This family consists of putative phage head proteins.
Virulence effector, SrfC (Vir_effector_SfrC)
Type: Family

This group represents a virulence effector protein, SrfC type. The function of this family is not known.
Predicted S-adenosyl-L-methionine dependent methyltransferase, YjhP-type (Pre_MeTrfase_YjhP)
Type: Family

This entry represents proteins predicted to function as S-adenosyl-L-methionine dependent methyltransferases, such as the uncharacterised protein YjhP from Escherichia coli.
Vi polysaccharide biosynthesis protein TviA (TviA)
Type: Family

TviA from Salmonella typhi is a transcriptional activator of the viaB operon and regulates virulence factors outside SPI-7, including the flagellar regulon . Gene regulation of virulence factors enables S. typhi to conceal a pathogen-induced process from being sensed by the inflammasome, a protein complex responsible for activation of inflammatory processes .
Type III secretion system apparatus protein SsaM (T3SS_SsaM)
Type: Family

This group represents a type III secretion system apparatus protein SsaM. The product of the ssaM gene does not appear to be similar to products of other type III secretion systems .
Abortive infection system protein AbiD/AbiF (Abi_system_AbiD/AbiF)
Type: Family

Bacteria have numerous mechanisms to resist bacteriophage infection. While most are based on preventing infection in the first place, the abortive infection (Abi) systems provide protection by the abortion of an existing phage infection . Typically, these Abi systems target a crucial step of phage multiplication such as replication, transcription or translation, and lead to the death of the infected cell.

The AbiD protein provides resistance to phage infection by interfering with a phage-encoded endonuclease, while AbiF interferes with DNA replication .
Uncharacterised conserved protein UCP035009, HsdR, All3000-type (UCP035009_HsdR_All3000-type)
Type: Family

This group represents an uncharacterised protein with enzyme R HSDR_N domain, All3000 type.
Lmo0553-like (Lmo0553-like)
Type: Family

This entry represents Lmo0553 protein from Listeria monocytogenes (

) and similar proteins predominantly found in bacillales and lactobacillales. Lmo0553, now called CbpA, binds cyclic di-AMP, a signalling molecule, through its CBS (cystathionine-beta-synthase) domain .
Uncharacterised conserved protein UCP035261 (UCP035261)
Type: Family

This group represents an uncharacterised conserved protein.
Uncharacterised conserved protein UCP035609, HNH endonuclease-type (UCP035609_HNH_endonucl)
Type: Family

This group represents an uncharacterised protein with HNH endonuclease domain.
Virulence factor BrkB (Virul_fac_BrkB)
Type: Family

Members of this family include the largely uncharacterised BrkB (Bordetella resist killing by serum B) from Bordetella pertussis. It is essential for resistance to complement-dependent killing by serum in Bordetella pertussis . Some members have an additional C-terminal domain. Paralogs from E. coli (yhjD) and Mycobactrium tuberculosis (Rv3335c) are part of a smaller, related subfamily that form their own cluster .
Uncharacterised conserved protein UCP035918 , rubrerythrin/DUF125-related (UCP035918_rubreryth/DUF125)
Type: Family

This group represents a rubrerythrin-related protein with a transmembrane DUF125 domain (

).
Uncharacterised conserved protein UCP036054 (UCP036054)
Type: Family

There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function. Members of this entry are mainly found in proteobacteria.
Uncharacterised conserved protein UCP036055 (UCP036055)
Type: Family

There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function. Members of this entry are mainly found in proteobacteria.
Type I restriction-modification system, specificity subunit, predicted (HsdS_prd)
Type: Family

This group represents a predicted type I restriction-modification system, specificity subunit.
Uncharacterised conserved protein UCP036238 (UCP036238)
Type: Family

This group represents an uncharacterised conserved protein.
Maltose phosphorylase/glycosyl hydrolase/vacuolar acid trehalase (Malt_Pase/Glycosyl_Hdrlase)
Type: Family

This group represents a maltose phosphorylase/glycosyl hydrolase/vacuolar acid trehalase.
Prenylcysteine oxidase 1 (Prenylcysteine_Oxase1)
Type: Family

This entry represents prenylcysteine oxidases (also known as prenylcysteine lyases) and homologues that are predicted to have the same function. The human enzyme is part of the lysosome and functions in the degradation of prenylated proteins, cleaving the thioether bond of prenyl-L-cysteines, such as farnesylcysteine and geranylgeranylcysteine . More recently, prenylcysteine oxidase 1 (PCYOX1) has been found in apoB100-containing lipoproteins, having pro-oxidant activity. It may contribute to development of atherosclerosis, as it is able to generate reactive oxygen species (ROS) and, therefore, contribute lipoproteins oxidation .
Cripto (Cripto)
Type: Family

This entry represents Cripto proteins (also known as Teratocarcinoma-derived growth factor 1) found in mammals.

Cripto is a protein overexpressed in many tumours and structurally similar to the C-terminal extracellular portions of Jagged 1 and Jagged 2 .
Fibulin-1 (Fibulin-1)
Type: Family

Fibulins are a family of ECM glycoproteins characterised by a fibulin-type C-terminal domain preceded by tandem calcium-binding epidermal growth factor (EGF)-like modules. They are involved in protein-protein interactions with the components of the basement membrane and extracellular matrix proteins. There are five fibulins, which can be classified into two subgroups. Fibulin-1 and -2 constitute one subgroup. These fibulins are larger than the others due to the presence of a higher number of EGF modules and an extra domain with three anaphylatoxin modules . Members of the second subgroup, fibulin-3, -4, and -5, are similarly small in size and highly homologous to one another in modular structure. They consist of a modified cbEGF domain at the N terminus followed by five tandem cbEGF modules and the fibulin-type C-terminal region.

This entry represents the fibulin-1 proteins, which are incorporated into fibronectin-containing matrix fibres and may play a role in cell adhesion and migration .
Low density lipoprotein receptor-related protein 5/6 (LRP5/6)
Type: Family

LRP5/6 are transmembrane receptors that are involved in Wnt signal transduction . Binding of the Wnts to LRP5/6 and their participating co-receptors, the frizzled (Fz) family of 7 transmembrane spanning proteins, results in a series of downstream intracelullar events, in particular the inhibition by subsequent phosphorylation of GSK-3beta . LRP5/6 have been shown to play an role in bone homeostasis .

Mutations in the LRP5 gene cause vitreoretinopathy, exudative 4 (EVR4), a disorder of the retinal vasculature characterised by an abrupt cessation of growth of peripheral capillaries, leading to an avascular peripheral retina . Mutations in the LRP6 gene cause coronary artery disease, autosomal dominant, 2 (ADCAD2), a common heart disease characterised by reduced or absent blood flow in one or more of the arteries that encircle and supply the heart .
Metallopeptidase, nematode (Metallopeptidase_nem)
Type: Family

This family of metallopeptidases is found in nematodes and belongs to the wider peptidase M12A family. Mutant studies and RNAi analyses suggest that the family has an important role in the moulting process . The proteases are thought to be secreted by hypodermal cells and to participate in shedding of old cuticles.
Peptidase S1A, matripase (Peptidase_S1A_matripase)
Type: Family

This group represents matriptase, which is a type II transmembrane serine peptidase belonging to MEROPS peptidase family S1A (clan PA(S)). It is involved in a number of cellular processed that include: regulation of epithelial barrier formation and permeability in the intestine ; proteolytic cleavage of human acid-sensing ion channel 1 and the regulation of the matriptase-prostasin cell surface proteolytic cascade by hepatocyte growth factor activator inhibitor-1 during epidermal differentiation .