SII-SWORD/CoKE huggingface dataset:
CRISPR-associated protein Cas7, subtype I-B/Tneap, bacterial (Cas7/Cst2/DevR_bac)
Type: Family

CRISPR (clustered regularly interspaced short palindromic repeat) is an adaptive immune system that provides protection against mobile genetic elements (viruses, transposable elements and conjugative plasmids). CRISPR clusters contain spacers, sequences complementary to antecedent mobile elements, and target invading nucleic acids. CRISPR clusters are transcribed and processed into CRISPR RNA (crRNA). This entry represents the Cas7 (DevR) protein which has a role in fruiting body development, sporulation and aggregation. Expression begins by 6 hours after starvation has initiated development and is under strong negative autoregulation .
D-(-)-3-hydroxybutyrate oligomer hydrolase, putative (OHBut_olig_hydro_put)
Type: Family

This entry represents a group of predicted D-(-)-3-hydroxybutyrate oligomer hydrolases (also known as 3HB-oligomer hydrolase), which function in the degradation of poly-3-hydroxybutyrate (PHB). These enzymes catalyse the hydrolysis of D(-)-3-hydroxybutyrate oligomers (3HB-oligomers) into 3HB-monomers .
Uncharacterised conserved protein UCP011452, HNH endonuclease domain-type (UCP011452_HNH_endonucl)
Type: Family

There is currently no experimental data for members of this group or their homologues. However, they contain a version of the HNH endonuclease domain (

).
Methyltransferase VrtF-like (MeTrfase_VrtF)
Type: Family

This family contains methyltransferases from bacteria and fungi, including VrtF, AdaD, CtvB and VerB. The gene encoding O-methyltransferase VrtF is part of the gene cluster that mediates the biosynthesis of viridicatumtoxin, a tetracycline-like fungal polyketide . Similarly, the ctvB gene is part of a cluster that encode proteins for the biosynthesis of citreoviridin, an inhibitor of the F1-ATPase beta-subunit. CtvB methylates the alpha-pyrone hydroxyl group of an intermediate to generate citreomontanin . Methyltransferase VerB is encoded by of the gene cluster that mediates the biosynthesis of the neurotoxin verrucosidin, a methylated alpha-pyrone polyketide that inhibits oxidative phosphorylation in mitochondria and thereby causes neurological diseases . The adaD gene is part of the gene cluster that mediates the biosynthesis of the linear tetracyclic TAN-1612 neuropeptide Y receptor antagonist. AdaD is O-methyltransferase involved in Secondary metabolite biosynthesis .
Glycine/sarcosine/betaine reductase, component B, fused alpha/beta (Gly/sarc/bet_Rdtase_B_asu/bsu)
Type: Family

This group represents a glycine/sarcosine/betaine reductase, component B, fused alpha/beta subunits.
Mitochondrial transcription factor Mtf1 (Mtf1)
Type: Family

The yeast mitochondrial RNA polymerase (RNAP) is a two-subunit enzyme composed of a catalytic core (Rpo41) and a specificity factor (Mtf1) encoded by nuclear genes . Though related to RNA methyltransferases, Mtf1 might be a functional analogue of the bacterial initiation factor sigma . This group represents Mtf1 (mitochondrial transcription factor 1).
DNA damage checkpoint control protein Rad17 (Rad17)
Type: Family

This entry represents Rad17 from budding yeast (the homologue of human and S. pombe Rad1). Rad17 is a component of the checkpoint clamp complex (Ddc1/Mec3/Rad17) involved in the surveillance mechanism that allows the DNA repair pathways to act to restore the integrity of the DNA prior to DNA synthesis or separation of the replicated chromosomes . In S. cerevisiae, the Ddc1-Mec3-Rad17 complex associates with sites of DNA damage and modulates the Mec1 signaling pathway and the activation of Rad53 in response to DNA damage at phase G1 . The complex also physically regulates DNA polymerase zeta-dependent mutagenesis by controlling the access of polymerase zeta to damaged DNA . Contrary to its human counterpart, the 9-1-1 complex, the checkpoint clamp complex shows no detectable exonuclease activity .
Replication factor A protein 3, Saccharomycetes (Rfp3_Saccharomycetes)
Type: Family

This entry represents Rfa3 from budding yeasts. Rfa3 is a component of the replication protein A (RPA) complex, which binds to and removes secondary structure from ssDNA. The RPA complex is involved in DNA replication, repair, and recombination .
tRNA-splicing endonuclease, SEN2 subunit (tRNA_splic_SEN2)
Type: Family

This entry represents one of the two catalytic subunits of the tRNA-splicing endonuclease complex, a complex responsible for identification and cleavage of the splice sites in pre-tRNA. In at least some cases, the tRNA splicing endonuclease is also involved in mRNA processing via its association with pre-mRNA 3'-end processing factors, establishing a link between pre-tRNA splicing and pre-mRNA 3'-end formation, suggesting that the endonuclease subunits function in multiple RNA-processing events .
Rhamnogalacturonase B (Rhamnogalacturonase_B)
Type: Family

This entry represents rhamnogalacturonase B, a pectinolytic enzyme (endolyase;

) that hydrolyses the alpha-L-rhamnopyranosyl-(1,4)-alpha-D-galacturonopyranosyl glycosidic linkage by beta-elimination, thereby generating oligosaccharides terminating at the non-reducing end with a hex-4-enopyranosyluronic acid residue . This protein belongs to the polysaccharide lyase 4 family.
Suppressor of fused, eukaryotic (Suppressor_of_fused_euk)
Type: Family

Sufu, encoding the human ortholog of Drosophila suppressor of fused, appears to have a conserved role in the repression of Hedgehog signalling . It is a repressor of the Gli and Ci transcription factors of the Hedgehog signalling cascade , and functions by binding these proteins and preventing their translocation to the nucleus. Sufu has been found to be a tumour-suppressor gene that predisposes individuals to medulloblastoma by modulating the SHH signalling pathway . Homologues of Sufu have been found in bacteria, though their function is not currently known.

This entry is specific for the eukaryotic Sufu proteins and does not include any homolgous bacterial sequences.
Nibrin (Nibrin_met)
Type: Family

Nibrin (also known as Nbs1 or p95) plays an important role in the DNA damage response (DDR) and DNA repair. It is part of the nuclear MRN complex, which consists of Mre11, Rad50, and Nbs1, and is involved in double-strand break (DSB) repair, DNA recombination, maintenance of telomere integrity, cell cycle checkpoint control and meiosis . Mutations in the NBN gene coding for nibrin cause the Nijmegen Breakage Syndrome (NBS), a rare autosomal recessive disorder characterised by genomic instability and increased risk of haematopoietic malignancies .
Adenovirus 41, E3-31.6kDa (Adenovirus-41_E3-31.6kDa)
Type: Family

This entry is represented by human adenovirus 41, E3-31.6kDa; it is a family of uncharacterised viral proteins.
Bacteriophage T4, inh (Phage_T4_inh)
Type: Family

This group represents a the prohead protease inhibitor, inh (Gp21) of phage T4.
Surface-adhesin protein E, Pasteurellaceae (Adhesin_E_Pasteurellaceae)
Type: Family

This entry represents the surface-adhesin protein E from Pasteurellaceae. Adhesin E plays a role in pathogenesis . It binds to host proteins including plasminogen, vitronectin and laminin .
Protein of unknown function UCP012335 (UCP012335)
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 UCP012359 (UCP012359)
Type: Family

There is currently no experimental data to indicate the function of proteins in this family. Some family members appear to contain a merR-type HTH DNA-binding domain.
Uncharacterised conserved protein UCP012467 (UCP012467)
Type: Family

This group represents an uncharacterised conserved protein.
Uncharacterised conserved protein UCP012569 (UCP012569)
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 UCP012611 (UCP012611)
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 UCP012637 (UCP012637)
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 UCP012666 (UCP012666)
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 UCP012886 (UCP012886)
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.
High-affinity nitrate transporter (Transptr_NO3_Nar2)
Type: Family

This group represents a high affinity nitrate transporter component from plants. It includes high-affinity nitrate transporter 3.1 (NRT3.1 or NAR2.1) from Arabidopsis, which acts as a dual component transporter with NTR2 . The functional unit for high-affinity nitrate influx may be a tetramer consisting of two subunits each of NRT2.1 and NRT3.1 . NRT3.1 may be involved in targeting NRT2 proteins to the plasma membrane . Both NRT2.1 and NRT3.1 are coordinately down-regulated by high external nitrate .
Uncharacterised conserved protein UCP012943 (UCP012943)
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.
Protein SCAI, metazoan/viridiplantae (SCAI_metazoan/Viridiplantae)
Type: Family

This entry represents protein SCAI from metazoans and plants. SCAI is a transcriptional cofactor and tumour suppressor that suppresses MKL1-induced SRF transcriptional activity. It may function in the RHOA-DIAPH1 signal transduction pathway and regulate cell migration through transcriptional regulation of ITGB1 .
PR domain zinc finger protein 1 (PRDM1)
Type: Family

PR domain zinc finger protein 1 (PRDM1, also known as BLIMP-1) is a transcriptional repressor that is essential for cellular development. This entry includes BLIMP-1 from vertebrates and its homologues from invertebrates.
Pleckstrin homology domain protein Opy1 (Opy1)
Type: Family

This entry includes budding yeast overproduction-induced pheromone-resistant yeast protein 1 (Opy1), which blocks the G1 arrest in the presence of mating pheromone . It binds phosphatidylinositol 4,5-bisphosphate (PtdIns(4,5)P2/PIP2) at the cell membrane and negatively regulates the activity of phosphatidylinositol 4-phosphate 5-kinase MSS4 .
Exonuclease V, Saccharomyces (Exo5)
Type: Family

This entry represents Exo5 and matches mainly Saccharomyces proteins.

In Saccharomyces cerevisiae (Baker's yeast), Exo5 is a single strand DNA specific 5'-exonuclease, which is involved in mitochondrial DNA replication and recombination. It has the capacity to slide across 5' double-stranded DNA or 5'RNA sequences and resumes cutting two nucleotides downstream of the double-stranded-to-single-stranded junction or RNA-to-DNA junction, respectively . It degrades single-stranded, but not double-stranded, DNA from the 5'-end, and the products are dinucleotides, except the 3'-terminal tri- and tetranucleotides, which are not degraded. The initial hydrolytic cut of exonuclease V on the dephosphorylated substrate produces a mixture of dinucleoside monophosphates and trinucleoside diphosphates . Exo5 is specific for single-stranded DNA and does not hydrolyze RNA .
Mitochondrial intermembrane space cysteine motif-containing protein Mix14 (Mix14)
Type: Family

Mix14 is a mitochondrial intermembrane space protein with unknown function .
Increased recombination centres protein 19 (Irc19)
Type: Family

Irc19 is involved in sporulation and maintenance of the mitochondrial DNA .
Mitochondrial holo-[acyl-carrier-protein] synthase Ppt2 (PPTase_2)
Type: Family

Ppt2 is a phosphopantetheine:protein transferase (PPTase) that transfers the 4'-phosphopantetheine moiety from coenzyme A to a Ser of mitochondrial acyl-carrier-protein .
Bardet-Biedl syndrome 2 protein (Bardet-Biedl_syndrome_2_prot)
Type: Family

This entry represents BBS2, which is required for leptin receptor signalling in the hypothalamus . BBS2 and 4 are also required for the localisation of somatostatin receptor 3 and melanin-concentrating hormone receptor 1 into neuronal cilia .

Bardet-Biedl syndrome is a member of genetic ciliopathies, but the link between cilia/centrosome deficits and metabolic abnormalities is not completely clear . Bardet-Biedl syndrome (BBS) is a heterogeneous genetic disorder characterised by many features, including retinal degeneration, obesity, cognitive impairment, polydactyly, renal abnormalities, and hypogenitalism. BBS genes play an important role in maintaining leptin sensitivity in proopiomelanocortin neurons . A relatively high incidence of BBS is found in the mixed Arab populations of Kuwait and in Bedouin tribes throughout the Middle East, most likely due to the high rate of consaguinity in these populations and a founder effect.

Primary cilia are ubiquitous cellular appendages that provide important sensory and signalling functions and their dysfunction underlies numerous human genetic disorders. The proteins disrupted in the human ciliary disorder Bardet-Biedl syndrome (BBS) are required for the localisation of G protein-coupled receptors to primary cilia on central neurons. The alteration of signalling caused by mislocalisation of ciliary signalling proteins underlies the BBS phenotype . Of the 12 known BBS genes, BBS1 is the most commonly mutated .
Armadillo repeat-containing protein 1 (ARMC1)
Type: Family

This entry includes Armadillo repeat-containing protein 1 (ARMC1) may play a role in determining mitochondrial length, distribution and motility and, therefore, may regulate mitochondrial dynamics. It may act in association with mitochondrial contact site and cristae organizing system (MICOS) complex components and mitochondrial outer membrane sorting assembly machinery (SAM) complex components .
Uncharacterised conserved protein UCP014422 (UCP014422)
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 UCP014439, ACT (UCP014439_ACT)
Type: Family

This group represents an uncharacterised protein with ACT domain.
CRISPR system ring nuclease SSO1393 (SSO1393)
Type: Family

This entry represents a family of archaeal proteins, including CRISPR system ring nuclease SSO1393 from Sulfolobus solfataricus (

).

SSO1393 has been described as a component of the CRISPR system . CRISPR (clustered regularly interspaced short palindromic repeat) is an adaptive immune system that provides protection against mobile genetic elements (viruses, transposable elements and conjugative plasmids) .
Uncharacterised conserved protein UCP014543 (UCP014543)
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.
Bacteriophage SP-beta, YorJ (Phage_SP-beta_YorJ)
Type: Family

This entry is represented by Bacteriophage SP-beta, YorJ. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.

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 UCP014753 (UCP014753)
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 UCP014872, subtilisin-related (UCP014872_subtilisin-rel)
Type: Family

This group represents uncharacterised conserved proteins related to the subtilisins.
Uncharacterised conserved protein UCP014897, archaea (UCP014897_arc)
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 UCP015013 (UCP015013)
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.
ATPase, SAG2001, predicted (ATPase_SAG2001_prd)
Type: Family

This group represents a predicted ATPase, SAG2001 type.
TATA box-binding protein-associated factor RNA polymerase I subunit A, chordata (RNA_pol_I_TAF1A/TAFI48_chr)
Type: Family

This entry represents subunit A (TATA-binding protein-associated factor TAFI48 or TAF1A) of RNA polymerase I. It is a component of the transcription factor SL1/TIFIB complex involved in the assembly of the pre-initiation complex (PIC). The SL1/TIFIB complex is composed of TBP (TATA-binding protein) and TAF1A (TAFI48), TAF1B (TAFI63) and TAF1C (TAFI110) .

Human ribosomal RNA synthesis by RNA polymerase I requires the activator UBF and the promoter selectivity factor SL1/TIFIB. Both TAF1B/TAFI63 and TAF1C/TAFI110 contact the promoter, whereas TAF1A/TAFI48 serves as a target for interaction with UBF and is required to form a transcriptionally active SL1/TIFIB complex responsive to UBF . Interaction of the SL1/TIFIB subunits with TBP excluded interaction with the transcription factor IID (TFIID) subunits . This mutually exclusive binding directs the formation of promoter- and RNA polymerase-selective TBP-TAF complexes. Therefore, TAF1A/TAFI48 may function both as a target to mediate UBF activation and as a class-specific promoter selectivity factor.
Uncharacterised conserved protein UCP015278 (UCP015278)
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.
Regulatory, RpfE (Regulatory_RpfE)
Type: Family

This group represents a regulatory protein, RpfE type.
Conserved oligomeric Golgi complex subunit 8, Metazoal and Viridiplantae (COG8_Metazoal_Plant)
Type: Family

This entry represents conserved oligomeric Golgi complex subunit 8 from metazoans and viridiplantae. It is a component of the peripheral membrane COG complex that is involved in intra-Golgi protein trafficking .
Protein-arginine rhamnosyltransferase EarP (EarP)
Type: Family

This entry includes family members such as EarP enzymes which are essential for post-translational activation of elongation factor P (EF-P). It was identified as EF-P arginine R32 specific rhamnosyl transferase in Shewanella oneidensis using dTDP-beta-L-rhamnose as donor substrate . This was further confirmed for Pseudomonas aeruginosa , Pseudomonas putida and Neisseria meningitidis . As for S. oneidensis and P. aeruginosa , EarP enzyme acts as an inverting glycosyltransferase, thus mediating the formation of an alpha-L-rhamnosidic linkage. Structural analysis show that EarP is composed of two opposing domains with Rossmann folds, thus constituting a B pattern-type glycosyltransferase (GT-B) and provide basis for arginine glycosylation by EarP . Mutational analysis of efp and earP genes, resulted in a substantial decrease in the production of rhamnolipids and pyocyanin (important factors for colonization and invasion during infection) of P. aeruginosa. Collectively this indicates that EarP and EF-P are essential for P. aeruginosa pathogenicity . The protein family is also annotated in the CaZy Database as GT104.
DNA-binding transcriptional repressor CapW-like (CapW-like)
Type: Family

This entry represents DNA-binding transcriptional repressor CapW from Escherichia coli and similar WYL domain containing proteins mainly found in proteobacteria. CapW is a transcriptional regulator of a CBASS (cyclic oligonucleotide-based antiphage signaling system) antivirus system that provides immunity against bacteriophages .
Adaptor protein complex, sigma subunit (AP_complex_ssu)
Type: Family

The adaptor protein complexes mediate both the recruitment of clathrin to membranes and the recognition of sorting signals within the cytosolic tails of transmembrane cargo molecules . Adaptor protein complex 1 (AP-1) is a heterotetramer composed of two large adaptins (gamma-type subunit AP1G1 and beta-type subunit AP1B1), a medium adaptin (mu-type subunit AP1M1 or AP1M2) and a small adaptin (sigma-type subunit AP1S1 or AP1S2 or AP1S3). Subunits of clathrin-associated adaptor protein complex 1 play a role in protein sorting in the late-Golgi/trans-Golgi network (TGN) and/or in endosomes.

This group represents an adaptor protein complex, sigma subunit.
3-oxo-5-alpha-steroid 4-dehydrogenase (3-oxo-5-alpha-steroid_4-DH)
Type: Family

Synonym(s): Steroid 5-alpha-reductase

3-oxo-5-alpha-steroid 4-dehydrogenases,

catalyse the conversion of 3-oxo-5-alpha-steroid + acceptor to 3-oxo-delta(4)-steroid + reduced acceptor. The steroid 5-alpha-reductase enzyme is responsible for the formation of dihydrotestosterone, this hormone promotes the differentiation of male external genitalia and the prostate during foetal development . In humans mutations in this enzyme can cause a form of male pseudohermaphorditism in which the external genitalia and prostate fail to develop normally.

This family also includes the plant related steroid reductases DET2, involved in a reduction step in the biosynthesis of the plant steroid, brassinolide (BL) . DET2 from Brachypodium distachyon participates in the reduction steps of the biosynthesis of plant campesterol-derivative steroids, ending to castasterone (CS) but missing BL .
Neurogenic differentiation factor NeuroD (TF_bHLH_NeuroD)
Type: Family

NeuroD is a group of basic helix-loop-helix transcription factors.They mediate neuronal differentiation .
Uncharacterised protein family UPF0376 (UPF0376)
Type: Family

This entry represents a group of uncharacterised proteins found in Caenorhabditis spp. This entry includes Excretory canal abnormal exc-13 from Caenorhabditis elegans (

).
Glutathione S-transferase Omega/GSH (GST_Omega/GSH)
Type: Family

This entry represents the predicted glutathione S-transferase omega-like protein and the glutathionyl-hydroquinone reductase YqjG. Glutathione S-transferase omega-like proteins active as '1-Cys' thiol transferase against beta-hydroxyethyl disulfide (HED), as dehydroascorbate reductase and as dimethylarsinic acid reductase, while not active against the standard GST substrate 1-chloro-2,4-dinitrobenzene (CDNB) . YqjG catalyses glutathione (GSH)-dependent reduction of glutathionyl-hydroquinones (GS-HQs) to the corresponding hydroquinones .
Nascent polypeptide-associated complex subunit alpha-like (EGD2/NACA0like)
Type: Family

In Saccharomyces cerevisiae, nascent polypeptide-associated complex subunit alpha (also known as EGD2) is a component of the nascent polypeptide-associated complex (NAC), a dynamic component of the ribosomal exit tunnel, protecting the emerging polypeptides from interaction with other cytoplasmic proteins to ensure appropriate nascent protein targeting .

In human and mouse, nascent polypeptide-associated complex subunit alpha (known as NACA) prevents inappropriate targeting of non-secretory polypeptides to the endoplasmic reticulum (ER). It binds to nascent polypeptide chains as they emerge from the ribosome and blocks their interaction with the signal recognition particle (SRP), which normally targets nascent secretory peptides to the ER .