SII-SWORD/CoKE huggingface dataset:
Minor tail T (Phage_tail_T)
Type: Domain

This entry represents the 'T' domain of the tail assembly protein GT from lambda-like viruses and their prophage.

In bacteriophage lambda, the overlapping open reading frames G and T are expressed by a programmed translational frameshift to produce the tail assembly proteins G and GT . Tail assembly protein GT shares it's N-terminal residues with tail assembly protein G, followed by residues of unique sequence . An analogous frameshift is widely conserved among other dsDNA tailed phages in their corresponding 'G' and 'GT' tail genes even in the absence of detectable sequence homology . The lambda tail assembly protein G and frameshift product GT are produced in a molar ratio of approximately 30:1. The correct molar ratio of these two related proteins, normally determined by the efficiency of the frameshift, is crucial for efficient assembly of functional tails . Although tail assembly proteins G and GT are both required for assembly of functional tails, neither is present in mature tails .
DNA glycosylase AlkZ-like (AlkZ-like)
Type: Family

This protein family includes Interstrand DNA cross-link repair glycosylase (YcaQ) from Escherichia coli, AlkZ from Streptomyces sahachiroi (also known as Azi36), and similar proteins predominantly found in bacteria. YcaQ is a DNA glycosylase that protects cells against the toxicity of agents causing interstrand DNA crosslinks (ICLs), a toxic form of DNA damage . The crystal structure of AlkZ revealed a C-shaped configuration with three tandem winged helix-turn-helix (wHTH) motifs and a positively charged surface that shows residues of great importance for the enzymatic activity .
Orthopoxvirus, Protein N1 (Orthopox_N1)
Type: Family

This family represents Protein N1 and similar proteins from the genus Orthopoxvirus. N1 is a Bcl-2-like protein which contributes to virulence by preventing host NF-kappa-B activation in response to pro-inflammatory stimuli such as TNF-alpha or IL1B .
Usg-like (Usg)
Type: Family

This is a family of bacterial proteins, referred to as Usg. Usg is found in the same operon as trpF, trpB, and trpA and is expressed in a coupled transcription-translation system .
Toluene-4-monooxygenase system B (Toluene_mOase_B)
Type: Family

This family includes several toluene-4-monooxygenase system (

) protein B (TmoB) sequences. Pseudomonas mendocina KR1 metabolises toluene as a carbon source. The initial step of the pathway is hydroxylation of toluene to form p-cresol by a multicomponent toluene-4-monooxygenase (T4MO) system .

Also included in the family is subunit gamma of the alkene monooxygenase multicomponent enzyme system (

) from Xanthobacter autotrophicus which catalyzes the O
2
- and NADH-dependent epoxidation of short chain (C2 to C6) alkenes to their corresponding epoxides .
NADH dehydrogenase subunit 4L (NAD_DH_su4L)
Type: Family

This family consists of NADH dehydrogenase subunit 4L (NAD4L) proteins from the mitochondria of several parasitic flatworms.
Solute carrier family 52, riboflavin transporter (Riboflavin_transptr)
Type: Family

This entry includes a group of animal riboflavin transporters, including SLC52A1, SLC52A2 and SLC52A3 from humans which belong to the MFS superfamily . They are plasma membrane proteins that transport vitamin B2 (riboflavin, RF) into cells . In case of infection by retroviruses, they act as cell receptors to retroviral envelopes similar to the porcine endogenous retrovirus (PERV-A) . Mutations in these transporters are associated with Brown-Vialetto-Van Laere Syndrome (BVVLS), a rare neurological disorder characterised by progressive pontobulbar palsy, sensorineural hearing loss and respiratory insufficiency .
1,2-phenylacetyl-CoA epoxidase, subunit B (PaaB)
Type: Family

This entry represents the 1,2-phenylacetyl-CoA epoxidase, subunit B (also known as PaaB) and related bacterial proteins.

Phenylacetyl-CoA monooxygenase (epoxidase) is a multicomponent enzyme, PaaABC(D)E, responsible for the hydroxylation of phenylacetate-CoA (PA-CoA) as the second catabolic step in phenylacetic acid (PA) degradation . Not only transforms phenylacetyl-CoA into its ring-1,2-epoxide, but also mediates the NADPH-dependent removal of the epoxide oxygen, regenerating phenylacetyl-CoA with formation of water .

The PaaB subunit probably acts as an effector protein .
Pre-mRNA-splicing factor Isy1 (Isy1)
Type: Family

This entry includes yeast Isy1 and it's homologues from plants and animals. In budding yeast, Isy1 is part of the NineTeen Complex (NTC), which is involved in spliceosome activation by specifying the interaction of U5 and U6 with pre-mRNA for their stable association with the spliceosome after U4 dissociation . The S. pombe homologue is known as Cwf12.
Centromere/kinetochore protein zw10, N-terminal (Zw10_N)
Type: Domain

This domain is found N-terminal in homologues of Centromere/kinetochore protein ZW10.

Zeste white 10 (ZW10) was initially identified as a mitotic checkpoint protein involved in chromosome segregation, and then implicated in targeting cytoplasmic dynein and dynactin to mitotic kinetochores, but it is also important in non-dividing cells. These include cytoplasmic dynein targeting to Golgi and other membranes, and SNARE-mediated ER-Golgi trafficking . Dominant-negative ZW10, anti-ZW10 antibody, and ZW10 RNA interference (RNAi) cause Golgi dispersal. ZW10 RNAi also disperse endosomes and lysosomes .

Drosophila kinetochore components Rough deal (Rod) and Zw10 are required for the proper functioning of the metaphase checkpoint in flies and mammals . The eukaryotic spindle assembly checkpoint (SAC) monitors microtubule attachment to kinetochores and prevents anaphase onset until all kinetochores are aligned on the metaphase plate. It is an essential surveillance mechanism that ensures high fidelity chromosome segregation during mitosis. In higher eukaryotes, cytoplasmic dynein is involved in silencing the SAC by removing the checkpoint proteins Mad2 and the Rod-Zw10-Zwilch complex (RZZ) from aligned kinetochores .
YhcG PDDEXK nuclease domain (YhcG_C)
Type: Domain

This domain can be found in uncharacterised proteins in viruses, archaea and bacteria, most notably it is found in YhcG protein from E.coli. This entry represents the C-terminal PDDEXK domain belonging to the PD-(D/E)XK superfamily of nucleases involved in DNA recombination and repair . Profile HMM analysis identified a relationship between this C-terminal domain of YhcG and endonuclease NucS . YhcG was identified in association with DNA processing enzymes, including the restriction complexes HsdMRS and McrABC, the integrases IntF and IntS, and the recombinase PinE .
Bacteriophage Mu, Gp16 (Phage_Mu_Gp16)
Type: Family

This family consists of several bacterial and phage proteins, including GemA (also known as gp16) protein from Bacteriophage Mu. GemA is an early protein responsible for decreasing host DNA gyrase activity, that promotes DNA relaxation of bacterial host genome. Modulates the expression of various host genes probably controlled by supercoiling of their promoters. Host genes affected include DNA replication and cell division determinants . This family also includes the Mu-like prophage FluMu protein gp16 from Haemophilus influenzae.
YdaT-like (YdaT-like)
Type: Family

YdaT is a transcriptional regulator whose expression significantly impairs bacterial growth and cell viability. It disrupts the expression of multiple regulons normally governed by RcsA, leading to defects in lipopolysaccharide biosynthesis and cell division. While YdaT has no impact on Rac prophage excision, its overexpression, particularly as part of the ydaST operon, has been linked to increased toxicity, morphological abnormalities, and further reductions in cell viability . YdaT toxin was first thought to be neutralised by the putative antitoxin YdaS (

) but recent studies showed that both YdaS and YdaT can act independently as toxins and are regulated by RacR .
Nucleopolyhedrovirus LEF-12 (Nucleo_LEF-12)
Type: Family

This family consists of several Nucleopolyhedrovirus late expression factor-12 (LEF-12) proteins. The function of this family is unknown .
Protein Veg (Protein_Veg)
Type: Family

VEG protein is highly conserved among Gram-positive bacteria. It stimulates biofilm formation through inducing transcription of the tapA-sipW-tasA operon. The products of this operon are responsible for production of the amyloid fibre (TasA) component of the biofilm. Veg or a Veg-induced protein acts as an antirepressor of SinR - part of the major overall biofilm transcriptional control system - to regulate and stimulate biofilm formation. Veg is transcribed at high levels during both exponential growth and sporulation .
Mitochondrial fission protein ELM1-like (Elm1-like)
Type: Family

In plants, this family is involved in mitochondrial fission. It binds to dynamin-related proteins and plays a role in their relocation from the cytosol to mitochondrial fission sites . Its function in bacteria is unknown.
Protein of unknown function DUF1024 (DUF1024)
Type: Family

This family consists of several hypothetical proteins, mainly Staphylococcus aureus phage phi proteins which are related to Orf64 from Staphylococcus phage 92 (Bacteriophage 92). The function of this family is unknown.
Actinobacillus actinomycetemcomitans leukotoxin activator LktC (LktC)
Type: Family

This family consists of several Actinobacillus actinomycetemcomitans leukotoxin activator (LktC) proteins. Actinobacillus actinomycetemcomitans is a Gram-negative bacterium that has been implicated in the etiology of several forms of periodontitis, especially localised juvenile periodontitis. LktC along with LktB and LktD are thought to be required for activation and localisation of the leukotoxin .
YutD-like (YutD-like)
Type: Family

This family contains a group of uncharacterised bacterial proteins, including YutD from Bacillus subtilis (PDBe:2kl5), a probable antitoxin component of a putative type VII toxin-antitoxin (TA) system, that probably neutralizes cognate toxin YutE.
Type III secretion protein HrpF (T3SS_HrpF)
Type: Family

The species Pseudomonas syringae encompasses plant pathogens with differing host specificities and corresponding pathovar designations. P. syringae requires the Hrp (type III protein secretion) system, encoded by a 25-kb cluster of hrp and hrc genes, in order to elicit the hypersensitive response (HR) in nonhosts or to be pathogenic in hosts. The exact function of HrpF is unknown but the protein is needed for pathogenicity .
Poxvirus virion membrane protein A14.5 (Poxvirus_A14.5)
Type: Family

This is a family of Poxvirus proteins. It includes virion membrane protein A14.5 from Vaccinia virus, also known as Virion membrane protein OPG141, which has been shown to enhance virulence in mice .
Circovirus 2, Orf5 (Circovirus2_Orf5)
Type: Family

This family consists of several short Circovirus proteins of unknown function.
Eukaryotic translation initiation factor 3 subunit K (eIF3k)
Type: Family

Eukaryotic translation initiation factor 3 subunit K is a Component of the eukaryotic translation initiation factor 3 (eIF-3) complex, which is involved in protein synthesis and, together with other initiation factors, stimulates binding of mRNA and methionyl-tRNAi to the 40S ribosome .
Protein of unknown function DUF1031 (DUF1031)
Type: Family

This family of uncharacterised proteins is found mostly in Lactococcus species and their bacteriophages.
Ethanolamine ammonia-lyase reactivase EutA (EutA)
Type: Family

Proteins in this entry are EutA ethanolamine utilization proteins, reactivating factors for ethanolamine ammonia lyase, encoded by the ethanolamine utilization eut operon .

The holoenzyme of adenosylcobalamin-dependent ethanolamine ammonia-lyase (EutBC,

,

), which is part of the ethanolamine utilization pathway , undergoes suicidal inactivation during catalysis as well as inactivation in the absence of substrate. The inactivation involves the irreversible cleavage of the Co-C bond of the coenzyme. The inactivated holoenzyme undergoes rapid and continuous reactivation in the presence of ATP, Mg2+, and free adenosylcobalamin in permeabilised cells (in situ), homogenate, and cell extracts of Escherichia coli. The EutA protein is essential for reactivation. It was demonstrated with purified recombinant EutA that both the suicidally inactivated and O2-inactivated holoethanolamine ammonia lyase underwent rapid reactivation in vitro by EutA in the presence of adenosylcobalamin, ATP, and Mg2+ . The inactive enzyme-cyanocobalamin complex was also activated in situ and in vitro by EutA under the same conditions. Thus EutA is believed to be the only component of the reactivating factor for ethanolamine ammonia lyase. Reactivation and activation occur through the exchange of modified coenzyme for free intact adenosylcobalamin .

Bacteria that harbor the ethanolamine utilization pathway can use ethanolamine as a source of carbon and nitrogen. For more information on the ethanolamine utilization pathway, please see

,

.
Condensin II complex subunit H2, N-terminal (H2_N)
Type: Domain

This entry represents the N-terminal domain of the H2 subunit of the condensing II complex, found in eukaryotes but not in fungi.
Structural protein VP1/VP3 (VP1_VP3)
Type: Family

Sulfolobus virus-like particle SSV1 and its fusellovirus homologues can be found in many acidic (pH less than 4.0) hot springs (greater than 70 degrees C) around the world. SSV1 contains a 15.5-kb double-stranded DNA genome that encodes 34 proteins with greater than 50 amino acids . A site-specific integrase and a DnaA-like protein have been previously identified by sequence homology, and three structural proteins have been isolated from purified virus and identified by N-terminal sequencing (VP1, VP2, and VP3).
Protein of unknown function DUF1036 (DUF1036)
Type: Family

This entry consists of several hypothetical bacterial proteins of unknown function.
Trehalose catabolism protein, ThuA, prokaryote (Trehalose_catabolism_ThuA_prok)
Type: Family

This family consists of several bacterial thuA like proteins, including thuA from Sinorhizobium meliloti (

) . The S. meliloti thuA gene is part of the thu operon (thuEFGKAB) that codes for transport and utilization functions of the disaccharide trehalose. ThuA is an enzyme(s) involved in the conversion of disaccharides to their respective 3-keto derivatives .
Coleoptericin (Coleoptericin)
Type: Family

This family consists of several insect coleoptericin, acaloleptin, holotricin and rhinocerosin proteins which are all known to be antibacterial proteins . These all appear to be short, glycine-rich molecules, inducible by infection.
Protein of unknown function DUF1040 (DUF1040)
Type: Family

This family consists of several bacterial YihD proteins of unknown function .
Swarming motility protein SwrD-like (SwrD-like)
Type: Family

Bacillus subtilis SwrD increases flagellar torque and is necessary for swarming .
Protein PsiB (Plasmid_inh_PsiB)
Type: Family

During F plasmid conjugation, the SOS response is suppressed by PsiB, an F-plasmid-encoded protein that binds and sequesters free RecA to prevent filament formation. PsiB contains a central five-stranded anti-parallel β sheet that is buttressed by α helices from the N and C termini. Its structure is similar to CapZ, a eukaryotic actin filament capping protein .
Z-ring associated protein G-like (ZapG-like)
Type: Family

This entry represents Z-ring associated protein G from Escherichia coli (ZapG) and similar proteins predominantly found in gammaproteobacteria. ZapG is involved in cell division, cell envelope biogenesis and cell shape maintenance. It is a key regulator of cell envelope growth, playing a crucial role in coordinating cell width, elongation and division to maintain cell envelope integrity . It plays an important role in the lipopolysaccharide (LPS) assembly/transport . This family was previously known as DUF1043.
Toxin HigB-2 (HigB-2)
Type: Family

Bacterial toxin-antitoxin loci consist of two genes in an operon encoding a 'toxin' and an 'antitoxin' respectively. Ectopic expression of the toxins severely reduces cell growth and prevents colony formation. This entry includes HigB-2, one of the toxins found in Vibrio cholerae. It inhibits translation by cleavage of mRNA .
Photosystem II PsbY (PSII_PsbY)
Type: Family

This family represents the low molecular weight transmembrane protein PsbY found in PSII. In higher plants, two related PsbY proteins exist, PsbY-1 and PsbY-2, which appear to function as a heterodimer. In spinach and Arabidopsis, these two proteins arise from a single-copy nuclear gene that is processed in the chloroplast. By contrast, prokaryotic and organellar chromosomes encode a single PsbY protein, as found in cyanobacteria and red algae, indicating a duplication event in the evolution of higher plants . PsbY has two low manganese-dependent activities: a catalase-like activity and an L-arginine metabolising activity that converts L-arginine into ornithine and urea . In addition, a redox-active group is thought to be present in the protein. In cyanobacteria, PsbY deletion mutants have a slightly impaired PSII that is less capable of coping with low levels of calcium ions than the wild-type.

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

PSII is a multisubunit protein-pigment complex containing polypeptides both intrinsic and extrinsic to the photosynthetic membrane . Within the core of the complex, the chlorophyll and β-carotene pigments are mainly bound to the antenna proteins CP43 (PsbC) and CP47 (PsbB), which pass the excitation energy on to the reaction centre proteins D1 (Qb, PsbA) and D2 (Qa, PsbD) that bind all the redox-active cofactors involved in the energy conversion process. The PSII oxygen-evolving complex (OEC) oxidises water to provide protons for use by PSI, and consists of OEE1 (PsbO), OEE2 (PsbP) and OEE3 (PsbQ). The remaining subunits in PSII are of low molecular weight (less than 10kDa), and are involved in PSII assembly, stabilisation, dimerisation, and photo-protection .
Protein of unknown function DUF1045 (DUF1045)
Type: Family

This family consists of several hypothetical proteins from Agrobacterium, Rhizobium and Brucella species. The function of this family is unknown.
Macrodomain Ter protein, MatP (MatP)
Type: Family

This entry contains MatP (YcbG), which is a component of the MatP/MatS site-specific system that organises the Ter macrodomain (MD) in Escherichia coli (strain K12) and related enterobacteria during replication of the chromosome. In E. coli there are 23 matS sequences, located in the Ter region which is centred on dif. The matS consensus is a palindromic sequence 5'-GTGAC[AG][CT]GTCAC, which is the recognition sequence for MatP. MatP binds to the matS sequences; and is critical for Ter MD formation. Inactivation of matP causes severe defects in chromosome segregation and cell division revealing its role as a major organiser of the Ter MD .

Many bacteria have circular genomes that are large in comparison to their cellular dimensions; this imposes the necessity for compaction of the chromosome during cellular growth, replication, transcription, and segregation. Compaction of chromosomes results in the formation of structures called nucleoids. Nucleoids can be generated by a number of different processes: they include unrestrained DNA supercoiling, formation of a chromatin-like structure through the interaction of DNA binding proteins, condensation by structural maintenance of chromosomes (SMC)-like proteins, and macromolecular crowding . Chromosome replication and segregation are intimately linked and tightly controlled to ensure that daughter cells each receive a complete copy of the genome. Chromosomes have replication origin (Ori) and termination (Ter) regions that are diametrically opposed. During the process of chromosome replication and cell division the Ori and Ter regions form two macrodomains (MDs), the Ori MD is centred on migS, a 25 bp sequence, that acts as the cis-acting site for the bipolar positioning of oriC . The Ter MD is centred on dif (deletion-induced filamentation), which is a resolvase site that reduces chromosome multimers to monomers . The Ori and Ter MDs are insulated from one and other by non-structural regions and other nucleoids. Chromosome replication initiates bidirectionally from oriC. Within the Ori MD with sister chromatids being located in separate cell halves and with the Ter macrodomain anchored to the cell pole. Cell division occurs with the completion of replication of the Ter region and the subsequent separation of the two sister chromatids .
23S rRNA methylase leader peptide (ErmCL)
Type: Family

This family consists of several very short bacterial 23S rRNA methylase leader peptide (ErmCL) sequences. ermC confers resistance to macrolide-lincosamide streptogramin B antibiotics by specifying a ribosomal RNA methylase, which results in decreased ribosomal affinity for these antibiotics. ermC expression is induced by exposure to erythromycin and is controlled by an uORF encoding the leader peptide ErmCL . It has been shown that the four C-terminal ErmCL residues I6F7V8I9 are crucial for ribosome stalling and that translation is arrested likely due to the PTC adopting an inactive conformation that prevents peptide bond formation with the incoming Ser-tRNASer at the 10th ermCL codon position .
Drosophila ACP53EA (ACP53EA)
Type: Family

This family consists of several Drosophila ACP53EA accessory gland (seminal) proteins .
DNA repair protein MmcB-like (MmcB-like)
Type: Family

Proteins in this entry include MmcB (

) from Caulobacter crescentus. MmcB is required specifically for MMC-induced mutagenesis. Based on the structural analysis of a close homologue, MmcB is predicted to be an endonuclease .
Biogenesis of lysosome-related organelles complex 1 subunit 1 (BLOC1S1)
Type: Family

GCN5L1 (general control of amino acid synthesis 5-like 1), also known as BLOC1S1 (biogenesis of lysosome-related organelles complex 1 subunit 1). It is a component of the BLOC-1 complex, a complex required for normal biogenesis of lysosome-related organelles . GCN5L1 has been identified as a critical component of the mitochondrial protein acetylation programme . It acts as a nutrient-sensing regulator that controls mitochondrial content through coordinated regulation of mitochondrial biogenesis and autophagy .
Pigment-dispersing hormone (Pigment_DH)
Type: Family

This family consists of several eukaryotic pigment-dispersing hormone (PDH) proteins. The pigment-dispersing hormone (PDH) is produced in the eyestalks of Crustacea where it induces light-adapting movements of pigment in the compound eye and regulates the pigment dispersion in the chromatophores .
Vesiculovirus matrix (Vesiculo_matrix)
Type: Family

This family consists of several Vesiculovirus matrix proteins. The matrix (M) protein of vesicular stomatitis virus (VSV) expressed in the absence of other viral components causes many of the cytopathic effects of VSV, including an inhibition of host gene expression and the induction of cell rounding. It has been shown that M protein also induces apoptosis in the absence of other viral components. It is thought that the activation of apoptotic pathways causes the inhibition of host gene expression and cell rounding by M protein .