SII-SWORD/CoKE huggingface dataset:
Flagellar filament outer layer protein FlaA, Spirochaetes (FlaA_Spirochaetes)
Type: Family

Periplasmic flagella are the organelles of spirochete mobility, and are structurally different from the flagella of other motile bacteria. They reside inside the cell within the periplasmic space, and confer mobility in viscous gel-like media such as connective tissue . The flagella are composed of an outer sheath of FlaA proteins and a core filament of FlaB proteins. Each species usually has several FlaA protein species .
Photosystem I reaction center subunit V/PsaK, plant (PSI_PsaG/PsaK_pln)
Type: Family

Photosystem I (PSI) is an integral membrane protein complex that uses light energy to mediate electron transfer from plastocyanin to ferredoxin. It is found in the chloroplasts of plants and cyanobacteria. PSI is composed of at least 14 different subunits, two of which are small hydrophobic proteins of about 7 to 9 Kd and evolutionary related, PsaG (also known as PSI-G) and PsaK (also known as PSI-K), both integral membrane proteins. Cyanobacteria contain only PsaK . While cyanobacterial PSI have phycobilisomes to harvest light, eukaryotic PSI have a membrane-imbedded peripheral antenna .

This group represents Photosystem I reaction center subunits V (PsaG) and PsaK from plants.
RNA polymerase sigma-H factor (RNA_pol_sigma-H_factor)
Type: Family

This entry represents RNA polymerase sigma-H factor found in bacteria. Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released. The major sigma factor in most bacteria is sigma-A. Sigma-H, the sigH (spo0H) gene product, directs the transcription of several genes that function in the transition from exponential growth to stationary phase, including the initiation of spore formation and entry into the state of genetic competence .
K88 fimbrial protein A (K88_fimbrial_pA)
Type: Family

K88 is a fimbrial protein involved in colonization of the porcine intestine .
Opacity (Opacity)
Type: Family

Pathogenic Neisseria spp. possess a repertoire of phase-variable opacity proteins that mediate various pathogen/host cell interactions . These proteins are integral membrane proteins related to other porins and the Haemophilus influenzae OpA protein.
Transcription factor, GATA-2/3 (TF_GATA-2/3)
Type: Family

GATA transcription factors mediate processes of development, differentiation, and gene expression in multiple tissues and cell types. Vertebrate GATA factors have two highly conserved zinc finger motifs and recognise a six-nucleotide motif T/AGATAG/A in target genes. They are separated into two subfamilies: 1) GATA1, GATA2, and GATA3 and 2) GATA4, GATA5, and GATA6. Members of the GATA1/2/3 subfamily are expressed in developing blood cells, where they regulate differentiation-specific gene expression in hematopoiesis . This entry represents the GATA2 and GATA3.
Transcription factor GATA-4/5/6 (TF_GATA_4/5/6)
Type: Family

This entry represents the GATA family of transcription factors, such as GATA-4, GATA-5 and GATA-6. These transcription factors regulate critical steps of cellular differentiation during vertebrate development. GATA-4, 5 and 6 each contain two GATA-type zinc fingers, and are known to activate numerous enterocytic genes . Loss of GATA-4 and GATA-5 has been reported in human gastric and colon cancer .
Histone acetyltransferase GCN5/PCAF (GCN5/PCAF)
Type: Family

Eukaryotic GCN5 acetyltransferases influence diverse biological processes by acetylating histones and non-histone proteins and regulating chromatin and gene-specific transcription as part of multiprotein complexes. Vertebrate organisms, express two paralogous GCN5-like acetyltransferases, GCN5 and PCAF (also known as KAT2A and KAT2B), which is included in this entry . GCN5/PCAF is a component of the ATAC complex, a complex with histone acetyltransferase activity on histones H3 and H4 .
Sucrose/Glucosylglycerate phosphorylase-related (Sucrose_GGa_phosphorylase-rel)
Type: Family

This entry includes a group of sucrose phosphorylases, including sucrose 6(F)-phosphate phosphorylase (Tthe_1921) from Thermoanaerobacterium thermosaccharolyticum, as well as glucosylglycerate phosphorylase. Tthe_1921 catalyses the reversible phosphorolysis of sucrose 6(F)-phosphate. It also acts on sucrose, D-fructose, alpha-D-glucose 1-phosphate and D-fructose 6-phosphate . Glucosylglycerate phosphorylase (part of subfamily 18 of glycoside hydrolase family 13 (GH13_18) in CAZy) was previously thought to also function as a sucrose phosphorylase. However, subsequent studies have shown it to be a glucosylglycerate phosphorylase, and to have no activity on sucrose .
Transcription factor cyclic AMP-dependent, CRE-BP1-type (TF_CRE-BP1-typ)
Type: Family

This group represents transcription factors ATF-2 (CRE-BP1), ATF-7 (ATFa) and CREB5 (CRE-BPa), which bind to the cyclic AMP response element . They compose a subfamily within the AP-1 transcription factors family based on sequence conservation .
Type III secretion system, low calcium response, chaperone LcrH/SycD, subgroup (T3SS_Ca_resp_chp_LcrH/SycD_sub)
Type: Family

The type III secretion system of Gram-negative bacteria is used to transport virulence factors from the pathogen directly into the host cell and is only triggered when the bacterium comes into close contact with the host. Effector proteins secreted by the type III system do not possess a secretion signal, and are considered unique because of this. Yersinia spp. secrete effector proteins called YopB and YopD that facilitate the spread of other translocated proteins through the type III needle and the host cell cytoplasm . Both are believed to act as pore translocases, forming apertures in the host cell membrane and allowing the bacterium easy access to its cytoplasm. YopD also acts as a negative regulator of the Yersinia low-calcium response, and in turn is controlled by a chaperone, SycD . This protein also regulates YopB secretion. SycD is located on the Yop pathogenicity island of Yersinia spp., and is speculated to prevent a premature interaction between YopB, YopD and the calcium-response LcrV protein .

It has been speculated that a type III secretion mechanism also exists in Chlamydial species. With the sequencing of the Chlamydia trachomatis genome, several proteins similar to characterised type III proteins have emerged, including a SycD homologue . The Pseudomonas aeruginosa gene PcrH is also similar to the Yersinia chaperone, suggesting a comparable function.

Proteins in this entry are found in type III secretion operons. LcrH, from Yersinia is believed to have a regulatory function in the low-calcium response of the secretion system . The same protein is also known as SycD (SYC = Specific Yop Chaperone) for its chaperone role . In Pseudomonas, where the homologue is known as PcrH, the chaperone role has been demonstrated and the regulatory role appears to be absent . ScyD/LcrH contains three central tetratricopeptide-like repeats that are predicted to fold into an all-α-helical array .
Signal transduction histidine kinase, nitrate/nitrite-sensing (Sig_transdc_His_kin_NarX/NarQ)
Type: Family

Two-component signal transduction systems enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions . Some bacteria can contain up to as many as 200 two-component systems that need tight regulation to prevent unwanted cross-talk . These pathways have been adapted to response to a wide variety of stimuli, including nutrients, cellular redox state, changes in osmolarity, quorum signals, antibiotics, and more . Two-component systems are comprised of a sensor histidine kinase (HK) and its cognate response regulator (RR) . The HK catalyses its own auto-phosphorylation followed by the transfer of the phosphoryl group to the receiver domain on RR; phosphorylation of the RR usually activates an attached output domain, which can then effect changes in cellular physiology, often by regulating gene expression. Some HK are bifunctional, catalysing both the phosphorylation and dephosphorylation of their cognate RR. The input stimuli can regulate either the kinase or phosphatase activity of the bifunctional HK.

A variant of the two-component system is the phospho-relay system. Here a hybrid HK auto-phosphorylates and then transfers the phosphoryl group to an internal receiver domain, rather than to a separate RR protein. The phosphoryl group is then shuttled to histidine phosphotransferase (HPT) and subsequently to a terminal RR, which can evoke the desired response .

Signal transducing histidine kinases are the key elements in two-component signal transduction systems, which control complex processes such as the initiation of development in microorganisms . Examples of histidine kinases are EnvZ, which plays a central role in osmoregulation , and CheA, which plays a central role in the chemotaxis system . Histidine kinases usually have an N-terminal ligand-binding domain and a C-terminal kinase domain, but other domains may also be present. The kinase domain is responsible for the autophosphorylation of the histidine with ATP, the phosphotransfer from the kinase to an aspartate of the response regulator, and (with bifunctional enzymes) the phosphotransfer from aspartyl phosphate back to ADP or to water . The kinase core has a unique fold, distinct from that of the Ser/Thr/Tyr kinase superfamily.

This entry represents signal transduction histidine kinases involved in nitrate/nitrite-sensing, such as NarQ in Neisseria gonorrhoeae and NarX in Escherichia coli . The NarQ(HK)/NarP(RR) and the NarX(HK)/NarL(RR) appear to function in nitrate/nitrite sensing. NarL may be positively regulated by phosphorylation in the presence of nitrite and negatively regulated by dephosphorylation in the absence of nitrate.
Signal transduction histidine kinase, DegS (Sig_transdc_His_kinase_DegS)
Type: Family

Two-component signal transduction systems enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions . Some bacteria can contain up to as many as 200 two-component systems that need tight regulation to prevent unwanted cross-talk . These pathways have been adapted to response to a wide variety of stimuli, including nutrients, cellular redox state, changes in osmolarity, quorum signals, antibiotics, and more . Two-component systems are comprised of a sensor histidine kinase (HK) and its cognate response regulator (RR) . The HK catalyses its own auto-phosphorylation followed by the transfer of the phosphoryl group to the receiver domain on RR; phosphorylation of the RR usually activates an attached output domain, which can then effect changes in cellular physiology, often by regulating gene expression. Some HK are bifunctional, catalysing both the phosphorylation and dephosphorylation of their cognate RR. The input stimuli can regulate either the kinase or phosphatase activity of the bifunctional HK.

A variant of the two-component system is the phospho-relay system. Here a hybrid HK auto-phosphorylates and then transfers the phosphoryl group to an internal receiver domain, rather than to a separate RR protein. The phosphoryl group is then shuttled to histidine phosphotransferase (HPT) and subsequently to a terminal RR, which can evoke the desired response .

Signal transducing histidine kinases are the key elements in two-component signal transduction systems, which control complex processes such as the initiation of development in microorganisms . Examples of histidine kinases are EnvZ, which plays a central role in osmoregulation , and CheA, which plays a central role in the chemotaxis system . Histidine kinases usually have an N-terminal ligand-binding domain and a C-terminal kinase domain, but other domains may also be present. The kinase domain is responsible for the autophosphorylation of the histidine with ATP, the phosphotransfer from the kinase to an aspartate of the response regulator, and (with bifunctional enzymes) the phosphotransfer from aspartyl phosphate back to ADP or to water . The kinase core has a unique fold, distinct from that of the Ser/Thr/Tyr kinase superfamily.

This entry represents signal transduction histidine kinases such as DegS. The DegS histidine kinase acts in concert with DegU response regulator in the soil bacteria Bacillus subtilis. The resulting phosphorylated DegU can regulate the transcription of over 120 target genes, many of which encode enzymes that degrade polymeric carbon and nitrogen sources .
Pilus assembly, TraL (Pilus_assmbly_TraL)
Type: Family

This entry represents the bacterial F pilus assembly protein TraL . The F-pilus appears to be involved in recipient cell recognition during the establishment of a stable mating pair before conjugation, as well as forming part of the conjugative pore for DNA transfer . The F-pilus is the site of attachment of the filamentous phages (M13, f1 and fd), which attach to the F-pilus tip, and the RNA phages, R17 and Qbeta, which attach to different sites exposed on the sides of the pilus.
Plasmid transfer regulator TraJ (TraJ)
Type: Family

This entry represents the plasmid transfer regulator TraJ.
Plasmid transfer regulator TraJ, R1 plasmid (TraJ_R1)
Type: Family

This entry represents the plasmid transfer regulator TraJ found on R1 plasmids. In Escherichia coli, TraJ has a role in regulating the expression of transfer genes that are involved in the conjugal transfer of DNA between bacterial cells .
Conjugal transfer repressor TrbA (Conjugal_tfr_repressor_TrbA)
Type: Family

This group represents a conjugative transfer repressor TrbA.
Plasmid mobilisation, TrbF (Plasmid_mob_TrbF)
Type: Family

This group represents a plasmid mobilisation protein TrbF.
Mobilization, MobA (Mobilization_MobA)
Type: Family

This group represents a mobilisation protein MobA.
Putative partitioning protein SopC (Put_partitioning_SopC)
Type: Family

Proteins in this uncharacterised family are encoded in plasmids and could represent a partitioning protein SopC.
Exclusion-determining protein (Exclusion-determining_protein)
Type: Family

This group represents an exclusion-determining protein ExcA.
Coatomer subunit alpha (Coatomer_asu)
Type: Family

Proteins synthesised on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment. This traffic is bidirectional, to ensure that proteins required to form vesicles are recycled. Vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transfer . While clathrin mediates endocytic protein transport, and transport from ER to Golgi, coatomers primarily mediate intra-Golgi transport, as well as the reverse Golgi to ER transport of dilysine-tagged proteins . For example, the coatomer COP1 (coat protein complex 1) is responsible for reverse transport of recycled proteins from Golgi and pre-Golgi compartments back to the ER, while COPII buds vesicles from the ER to the Golgi . Coatomers reversibly associate with Golgi (non-clathrin-coated) vesicles to mediate protein transport and for budding from Golgi membranes . COPI coated vesicle assembly is initiated by recruitment of the small GTPase Arf1 which recruits the coatomer protein complex from the cytoplasm and anchors it at the membrane. Then, Arf1 is activated by a guanine exchange factor and hydrolyses GTP to mediate uncoating of the vesicle which subsequently fuses with its target membrane . As coat proteins polymerise, vesicles are formed and budded from membrane-bound organelles. Coatomer complexes also influence Golgi structural integrity, as well as the processing, activity, and endocytic recycling of LDL receptors. In mammals, coatomer complexes can only be recruited by membranes associated to ADP-ribosylation factors (ARFs), which are small GTP-binding proteins. Coatomer complexes are hetero-oligomers composed of at least an alpha, beta, beta', gamma, delta, epsilon and zeta subunits, and can be subdivided into an outer-coat and an adaptor subcomplex .

This group represents coatomer subunit alpha, a component of the coatomer, which is a cytosolic protein complex involved in biosynthetic protein transport from the endoplasmic reticulum in eukaryotic cells. Coatomer complexes are hetero-oligomers composed of at least an alpha, beta, beta', gamma, delta, epsilon and zeta subunit. It is a heptameric complex that can polymerize into a cage to deform the membrane into a bud. In mammals, the coatomer can only be recruited by membranes associated to ADP-ribosylation factors (ARFs), which are small GTP-binding proteins; the complex also influences the Golgi structural integrity, as well as the processing, activity, and endocytic recycling of LDL receptors.

Structural studies show the homo-oligomerization of this protein plays a key role in the stability of the coat complex . It is composed of β-propellers and extended α-solenoids .

In humans, defects in its expression are related to primary immunodeficiencies that lead to immune dysregulation, arthritis and interstitial lung disease . This protein has also been related to Alzheimer's disease .
Large T antigen, polyomaviridae (Lg_T_Ag_polyomavir)
Type: Family

The group of polyomaviruses is formed by the homonymous murine virus (Py) as well as other representative members such as the simian virus 40 (SV40) and the human BK and JC viruses . Their large T antigen (T-ag) protein binds to and activates DNA replication from the origin of DNA replication (ori). Insofar as is known, the T-ag binds to the origin first as a monomer to its pentanucleotide recognition element. The monomers are then thought to assemble into hexamers and double hexamers, which constitute the form that is active in initiation of DNA replication. When bound to the ori, T-ag double hexamers encircle DNA . T-ag is a multidomain protein that contains an N-terminal J domain, which mediates protein interactions (see

,

), a central origin-binding domain (OBD), and a C-terminal superfamily 3 helicase domain (see

,

) .

This group represents a large T antigen, Polyomaviridae type.

The oncogenic large tumour antigen (LTag) is a protein found in polyomaviruses which is essential for viral DNA replication . LTag contains three domains, an N-terminal DnaJ domain which mediates protein interactions (

), a domain which binds the origin of DNA replication (

), and a C-terminal helicase domain. Replication is intitated by LTag assembling at the origin as a double hexamer that distorts and melts the origin DNA . During elongation LTag acts as a helicase that unwinds duplex DNA at the replication forks .
Replication protein E1, papillomavirus (Rep_E1_papillomaV)
Type: Family

This group represents a replication protein E1, papillomavirus type.
Human herpesvirus 5, RL1 (HHV5_RL1)
Type: Family

This entry is includes a group of proteins from human cytomegalovirus HHV5, including Protein RL1, which degrades the host antiviral factor SLFN11 via the cullin4-RING E3 ubiquitin ligase (CRL4) complex .
Cytoplasmic envelopment protein 3, Simplexvirus (UL11_simplexvirus)
Type: Family

Cytoplasmic envelopment protein 3 (UL11) is conserved throughout the herpesvirus family. It is a membrane-associated tegument protein that is incorporated into the HSV virion. UL11 and UL51, either singly or in combination, are involved in virion envelopment and/or egress. Both proteins are fatty acylated. UL11 is both acylated by myristoic and palmitoic acids while UL51 is mono-acylated by palmitoic acid .].

UL11 participates also in viral entry at the fusion step probably by regulating the core fusion machinery . It binds to either to gE or gI, promote the transport of virus particles in neuronal axons .
Protein K3-like, poxvirus (K3-like_poxvir)
Type: Family

This entry represents proteins predicted to function as serpins from various poxviruses, such as protein K3 from Vaccinia virus. Serpins are serine protease inhibitors. Protein K3 plays an integral role in the resistance of the virus to interferon and may bind competitively to P1 kinase in order to block eIF-2-alpha phosphorylation .
E3 ubiquitin-protein ligase p28 (E3_ubiquitin-prot_ligase_p28)
Type: Family

This entry represents the viral E3 ubiquitin-protein ligase p28, also known as host range factor p28, which functions as a virulence factor .
Apoptosis regulator, T4-like (Apoptosis_reg_M-T4)
Type: Family

Apoptosis, or programmed cell death (PCD), is a common and evolutionarily conserved property of all metazoans . In many biological processes, apoptosis is required to eliminate supernumerary or dangerous (such as pre-cancerous) cells and to promote normal development. Dysregulation of apoptosis can, therefore, contribute to the development of many major diseases including cancer, autoimmunity and neurodegenerative disorders. In most cases, proteins of the caspase family execute the genetic programme that leads to cell death.

This group represents an ER-localized apoptosis regulator, M-T4 type. M-T4 has both an N-terminal signal sequence and a C-terminal -RDEL sequence, suggesting that M-T4 resides in the endoplasmic reticulum. M-T4 is an intracellular virulence factor in myxoma virus that functions from within the endoplasmic reticulum and is necessary for the productive infection of lymphocytes . The C-terminal RDEL motif of the myxoma virus M-T4 protein may not be solely responsible for retention of M-T4 in the ER. M-T4 may have a dual function in protecting infected lymphocytes from apoptosis and in modulating the inflammatory response to virus infection . Members of this entry belong to poxviruses.
Rev protein, Ovine/caprine lentivirus (Rev_lentivir)
Type: Family

This group represents Rev protein from Ovine/caprine lentiviruses . The Rev protein escorts unspliced or incompletely spliced viral pre-mRNAs (late transcripts) out of the nucleus of infected cells. These pre-mRNAs carry a recognition sequence called Rev responsive element (RRE) located in the env gene, that is not present in fully spliced viral mRNAs (early transcripts) . This function is essential since most viral proteins are translated from unspliced or partially spliced pre-mRNAs, which cannot exit the nucleus by the pathway used by fully processed cellular mRNAs. Rev protein is a homomultimer when bound to RRE, its multimeric assembly being essential for activity.
Envelope glycoprotein precursor, Hantavirus (Envelope_glycoprot_Hantavirus)
Type: Family

The medium (M) genome segment of Hantaviruses encodes the two virion glycoproteins , G1 and G2, as a polyprotein precursor. This entry represents the M polyprotein precursor.
M polyprotein precursor, phlebovirus (M_polyprot_prcur_phlebovir)
Type: Family

This group represents the Phlebovirus M polyprotein precursor that contains the nonstructural protein NS-M, glycoprotein G1 and glycoprotein G2.
Coat protein, Ilarvirus, predicted (Coat_Ilarvirus_prd)
Type: Family

This group represents a predicted coat protein found in ilarviruses.