SII-SWORD/CoKE huggingface dataset:
THO complex subunit Thp2 (THO_cplx_su_Thp2)
Type: Family

Thp2 is part of the THO complex (Thp2, Hpr1, Tho2 and Mft1). The THO complex is the central component of the TREX complex, which is a key player in the transport of mRNA from the nucleus to the cytoplasm . The THO complex plays a role in transcription elongation .
Protein of unknown function DUF2015 (DUF2015)
Type: Family

This entry represents uncharacterised proteins found in fungi.
Domain of unknown function DUF2016 (DUF2016)
Type: Domain

This entry represents the N-terminal of proteins that contain a ubiquitin domain mainly found in bacteria. This domain is usually found associated with

.
Oxidative stress regulator AosR (AosR)
Type: Family

This entry includes the oxidative stress regulator AosR from Mycobacterium, a transcription factor crucial for intra-mycobacterial redox homeostasis and protection against host-derived oxidative and nitrosative radicals . In response to oxidative stress, it interacts with the ECF sigma factor SigH and, in conjunction with SigH, binds to an auxiliary promoter upstream of mec-cysO-cysM, leading to the transcriptional activation of these genes encoding a non-canonical actinomycete-specific cysteine biosynthesis pathway . Increased production of cysteine protects mycobacteria cells from host phagocyte-derived oxidative and nitrosative stress, thus facilitating the mycobacterial growth in the host .
ARS binding protein 2 (ARS-binding_2)
Type: Family

This DNA-binding protein binds to the autonomously replicating sequence (ARS) binding element. It may play a role in regulating the cell cycle response to stress signals .
Protein of unknown function DUF2018 (DUF2018)
Type: Family

This entry represents proteins of unknown function. The crystal structure of HP0242, a hypothetical protein from Helicobacter pylori (Campylobacter pylori) has been determined. It reveals an acid-adaptive protein possibly of physiological significance when H. pylori colonises the human stomach. The protein adopts a unique four α-helical triangular conformations. The biologically active form is thought to be a tetramer. The gene exist in an operon along with 6 other genes where the gene products appear to be related to iron storage and haem biosynthesis .
DNA replication checkpoint mediator, MRC1 domain (Repl_chkpnt_MRC1_dom)
Type: Domain

This putative domain is found in the most conserved region in mediator of replication checkpoint protein 1. This protein is a component of the replisome and is required for Rad3-dependent activation of the checkpoint kinase Cds1 in response to replication fork arrest .
Kinetochore subunit Nkp2/Cnl2 (Nkp2/Cnl2)
Type: Family

This entry includes the inner kinetochore subunit Cnl2 from fission yeasts and Nkp2 from budding yeasts .
4-Methylmuconolactone methyl-isomerase (MeMu_Me-Isoase)
Type: Domain

4-methylmuconolactone methyl-isomerase (MmlI), also known as 4-carboxymethyl-4-methylbutenolide mutase, is a short, approx 115 residue, protein of two α helices and four β strands. It is involved in the catabolism of methyl-substituted aromatics via a modified oxo-adipate pathway in bacteria. The enzyme appears to be monomeric in some species and tetrameric in others . The known structure shows two copies of the protein form a dimeric α β barrel.
Domain of unknown function DUF2020 (DUF2020)
Type: Domain

Protein of unknown function found in bacteria.
Domain of unknown function DUF2019 (DUF2019)
Type: Domain

Protein of unknown function found in bacteria.
Saf-pilin pilus formation protein (Saf-pilin_pilus_formation)
Type: Domain

This domain consists of the adjacent Saf-Nte and Saf-pilin chains of the pilus-forming complex. Pilus assembly in Gram-negative bacteria involves a Donor-strand exchange mechanism between the C- and the N-termini of this domain. The C-terminal subunit forms an incomplete Ig-fold which is then complemented by the 10-18 residue N terminus of another, incoming, pilus subunit which is not involved in the Ig-fold. The N terminus sequences contain a motif of alternating hydrophobic residues that occupy the P2 to P5 binding pockets in the groove of the first pilus subunit .
Phytotoxin, PcF (Phytotoxin_PcF)
Type: Domain

PcF is a 52 residue protein factor of two α helices, containing a 4-hydroxyproline and three cysteine bridges. The presence of the hydroxyproline is unique in relation to other fungal phytotoxic proteins. The protein has a high content of acidic side-chains implying a lack of binding with lipid-rich components of membranes and appears to be an extracellular phytotoxin that causes leaf necrosis in strawberries.
Membrane anchor Opy2, N-terminal (Membrane_anchor_Opy2_N)
Type: Domain

Opy2p acts as a membrane anchor in the HOG signalling pathway . This entry represents a conserved N-terminal domain.
Protein of unknown function YopT (YopT)
Type: Family

The function of the YopT protein is not known, though it has been structurally characterised. The protein is a homo-dimer, with each monomer consisting of one α helix and three β strands.
Restriction endonuclease, type II, AlwI (Restrct_endonuc_II_AlwI)
Type: Family

There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements , as summarised below:

Type I enzymes (

) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (

) activities.

Type II enzymes (

) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase.

Type III enzymes (

) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (

).

Type IV enzymes target methylated DNA.

Type II restriction endonucleases (

) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four β-strands and one α-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin . However, there is still considerable diversity amongst restriction endonucleases . The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone .

This entry includes AlwI (recognises GGATC), Bsp6I (recognises GC^NGC), BstNBI (recognises GASTC), PleI(recognises GAGTC) and MlyI (recognises GAGTC) restriction endonucleases.
Structure-specific endonuclease subunit Slx4 (Structure-sp_endonuc_su_Slx4)
Type: Family

The Slx4 protein is a heteromeric structure-specific endonuclease found from fungi to mammals. Slx4 is a regulatory subunit of the SLX1-SLX4 structure-specific endonuclease that resolves DNA secondary structures generated during DNA repair and recombination . The SLX1-SLX4 complex has a preference for 5'-flap structures, and promotes symmetrical cleavage of static and migrating Holliday junctions (HJs) .
Restriction endonuclease, type II, Eco29kI (Restrct_endonuc_II_Eco29kI)
Type: Family

There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements , as summarised below:

Type I enzymes (

) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (

) activities.

Type II enzymes (

) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase.

Type III enzymes (

) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (

).

Type IV enzymes target methylated DNA.

Type II restriction endonucleases (

) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four β-strands and one α-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin . However, there is still considerable diversity amongst restriction endonucleases . The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone .

This entry the restriction endonuclease Eco29kI which recognises and cleaves CCGC^GG.
Restriction endonuclease, type II, Pab1 (Restrct_endonuc_II_Pab1)
Type: Domain

This family includes R.Pab1 from Pyrococcus abyssi. R.Pab1 is homodimeric and has a curved anti-parallel β-sheet, which forms a three dimensional shape resembling a 'half pipe' that is responsible for double-strand DNA-binding .
Restriction endonuclease, type II, Bpu10I (Restrct_endonuc_II_Bpu10I)
Type: Family

This entry includes Bpu10I which recognises and cleaves CCTNAGC (-5/-2)restriction endonucleases.
Restriction endonuclease, type II, BstXI (Restrct_endonuc_II_BstXI)
Type: Family

This entry represents the restriction endonuclease BstXI which recognises and cleaves at CCANNNNN^NTGG.
Restriction endonuclease, type II, LlaJI (Restrct_endonuc_II_LlaJI)
Type: Family

This entry includes LlaJI which recognises GACGC restriction endonucleases .
Uncharacterised protein family YfhO (Uncharacterised_YfhO)
Type: Family

The yfhO gene is transcribed in Difco sporulation medium and the transcription is affected by the YvrGHb two-component system . Some members of this family have been annotated as putative ABC transporter permease proteins.
Type III secretion system, pilus formation, HrpA (T3SS_pilus_HrpA)
Type: Family

HrpA is an essential component of the type III secretion system (TTSS) which pathogens use to inject virulence factors directly into their host cells, and to cause disease. The TTSS has an Hrp pilus appendage for channelling effector proteins through the plant cell wall and this pilus elongates by the addition of HrpA pilin subunits at the distal end .
Envelope glycoprotein, lentivirus (Envelope_glycop_lentivirus)
Type: Family

The proteins in this family are envelope glycoproteins from feline immunodeficiency retrovirus. The process of lentiviral envelope glycoprotein-mediated fusion of membranes is essential for viral entry and syncytia formation .
Cotton leaf-curl disease, DNA-betaC1 (CLCuD_DNA-betaC1)
Type: Domain

Cotton leaf-curl disease - CLCuD - is of major economic importance in cotton-growing areas of the far-east. The infectious agent appears to be a single-stranded DNA molecule of approx 1350 nucleotides in length, which, when inoculated with the Begomovirus into cotton, induces symptoms typical of CLCuD. This molecule requires the Begomovirus for replication and encapsidation . DNA beta encodes a single protein, betaC1. The intracellular distribution of betaC1 is consistent with the hypothesis that it has a role in transporting the DNA A of Begomovirus from the nuclear site of replication to the plasmodesmatal exit sites of the infected cell. The DNA beta-encoded protein, betaC1, is the determinant of both pathogenicity and suppression of gene silencing .
Glycosyltransferase family 87 (GT87)
Type: Family

The enzymes in this family are glycosyltransferases. PimE is involved in phosphatidylinositol mannoside (PIM) synthesis, a major class of glycolipids in all mycobacteria. PimE is a polyprenol-phosphate-mannose-dependent mannosyltransferase that transfers the fifth mannose of PIM . The family also includes alpha(1-->3) arabinofuranosyltransferase, invloved in the synthesis of of mycobacterial arabinogalactan .
Metaviral G glycoprotein (Metaviral_G_glycop)
Type: Domain

This is a viral attachment glycoprotein from region G of metaviruses. It is high in serine and threonine suggesting it is highly glycosylated .
Brinker DNA-binding domain (Brinker_DNA-bd)
Type: Domain

This DNA-binding domain is the first approx. 100 residues of the N-terminal end of Brinker. The structure of this domain in complex with DNA consists of four α-helices that contain a helix-turn-helix DNA recognition motif specific for GC-rich DNA. The Brinker nuclear repressor is a major element of the Drosophila Decapentaplegic morphogen signalling pathway .
White spot syndrome virus (WSSV), Orf116/126, N-terminal (WSSV_Orf116/126_N)
Type: Domain

VP9 is a protein containing a ferredoxin fold. Two dimers come together to form one asymmetric unit which possesses a DNA recognition fold and specific metal binding sites possibly for zinc. It is postulated that being a non-structural protein VP9 is involved in the transcriptional regulation of the White spot syndrome virus (WSSV), from which it comes. WSSV is the major viral pathogen in shrimp aquaculture . VP9 is found N-terminal to the

.
Dihaem cytochrome c (Dihaem_cytochrome-c)
Type: Family

Dihaem cytochrome c (DHC) is a soluble c-type cytochrome that folds into two distinct domains, each binding a single haem group and connected by a small linker region. Despite little sequence similarity, the N-terminal domain (residues 12-75) is a class I type cytochrome c, that binds one of the haems, but the domain surrounding the other haem is structurally unique. DHC binds electrostatically to an oxygen-binding protein, sphaeroides haem protein (SHP), as a component of a conserved electron transfer pathway. DHC acts as the physiological electron donor for SHP during phototrophic growth . In certain species DHC is found upstream of

.
Pheromone response, PrgU-like domain (Pheromone_resp_PrgU-like)
Type: Domain

PrgU is a protein of plasmid in origin expressed mainly in Enterococcus bacteria. It forms a six β-strand barrel with three accompanying α helices and is probably a homo-dimer in the cell . PrgU probably acts as a RNA-binding regulator that mitigates toxicity accompanying overproduction of PrgB-like adhesins, which are involved in conjugative transfer .
Uncharacterised protein YvfG (Uncharacterised_YvfG)
Type: Family

Yvfg is a hypothetical protein of 71 residues expressed in some bacteria. The monomer consists of two parallel α-helices, and the protein crystallises as a homodimer.
YorP protein (YorP)
Type: Family

YorP is a 71 residue protein found in bacteria. As it is also found in a bacteriophage it might be of viral origin. The structure is of an α helix between two of five β strands. The function is unknown.
Protein of unknown function DUF2024 (DUF2024)
Type: Family

This protein of 86 residues is expressed in bacteria. It consists of two α helices and four β strands. Its function is unknown.
tRNA-splicing endonuclease subunit Sen15 (tRNA-endonuc_su_Sen15)
Type: Domain

The Sen15 subunit of the tRNA intron-splicing endonuclease is one of the two structural subunits of this heterotetrameric enzyme. Residues 36-157 of this subunit possess a novel homodimeric fold. Each monomer consists of three α-helices and a mixed antiparallel/parallel β-sheet. Two monomers of Sen15 fold with two monomers of Sen34, one of the two catalytic subunits, to form an alpha2-beta2 tetramer as part of the functional endonuclease assembly .
Domain of unknown function DUF2023 (DUF2023)
Type: Domain

This protein of unknown function of approx.120 residues consists of three β strands and five α helices, thought to fold into a homo-dimer.
Bacteriophage Tuc2009, YjcQ (Phage_Tuc2009_YjcQ)
Type: Family

YjcQ is a protein of approx. 100 residues containing four α helices and three β strands. It is found in bacteria and also in the Lactococcus phage Tuc2009. In bacteria it appears to be under the regulation of SigD RNA polymerase which is responsible for the expression of many genes encoding cell-surface proteins related to flagellar assembly, motility, chemotaxis and autolysis in the late exponential growth phase. The exact function of YjcQ is unknown . However, it is thought to be the major head protein in viruses and is found in prophage in bacteria.
Domain of unknown function DUF2027 (DUF2027)
Type: Domain

Proteins with this domain are uncharacterised, but may be involved in DNA mismatch repair. The domain is similar to the Smr domain (

).
Protein of unknown function DUF2026 (DUF2026)
Type: Family

This protein of approx. 100 residues is found in bacteria. It contains up to five α helices and up to seven β strands and is probably monomeric. Its function is unknown.
Bacillus phage SPbeta, YonK (Phage_SP-beta_YonK)
Type: Domain

YonK protein is expressed by the bacterial prophage SPbetaC . It is a 63 residue protein that associates into a homo-octamer in the form of a β-stranded barrel with four outer helical features at points of the compass. Its function is unknown.
Sulfolobus spindle-shape virus 1 F-112 protein-like (SSV1_F112-like)
Type: Family

This entry is represented by Sulfolobus spindle-shape virus 1 (SSV1), F112 protein . This protein adopts a winged helix DNA binding fold containing an intrachain disulfide bond . The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Gp37/putative cytoplasmic protein STM4215 (Gp37/STM4215)
Type: Family

This protein consists of a unit of helices and β-sheets that crystallises into a beautiful asymmetrical dodecameric barrel-structure, of two six-membered rings one on top of the other. It is expressed in bacteria but is of viral origin, as it is found in phage BcepMu and is probably a pathogenesis factor . This entry also includes a putative cytoplasmic protein, STM4215, from Salmonella.
Regulatory protein YycH-like (YycI-like)
Type: Domain

The YycFG two-component system is the only signal transduction system in Bacillus subtilis known to be essential for cell viability. This system is highly conserved in low-G+C Gram-positive bacteria, regulating important processes such as cell wall homeostasis, cell membrane integrity, and cell division. Four other genes, yycHIJK, are organised within the same operon with yycF and yycG in B. subtilis.
Sororin protein (Sororin)
Type: Family

Sororin is an essential, cell cycle-dependent mediator of sister chromatid cohesion . The protein is nuclear in interphase cells, dispersed from the chromatin in mitosis, and interacts with the cohesin complex . This protein protects cohesin from WAPL, which otherwise releases cohesin from DNA . Also included in this entry is dalmatian, a sororin-related protein from Drosophila melanogaster that combines protein functions of Sororin and Shugoshin to promote and protect cohesion .
Argonaute-binding protein 1 (Arb1)
Type: Family

Arb1 is a component of the argonaute siRNA chaperone (ARC) complex which is required for histone H3K9 methylation, heterochromatin assembly and siRNA generation .
Chromosome transmission fidelity protein 8 (Ctf8)
Type: Family

Ctf8 is a component of the RFC-like complex CTF18-RFC which is required for efficient establishment of chromosome cohesion during S-phase and may load or unload POL30/PCNA. During a clamp loading circle, the RFC:clamp complex binds to DNA and the recognition of the double-stranded/single-stranded junction stimulates ATP hydrolysis by RFC .
Gti1/Pac2 family (Gti1/Pac2)
Type: Family

In Schizosaccharomyces pombe the Gti1 protein promotes the onset of gluconate uptake upon glucose starvation . The Pac2 protein controls the onset of sexual development, by inhibiting the expression of ste11, in a pathway that is independent of the cAMP cascade .
Bud13 (Bud13)
Type: Family

Bud site selection protein 13, also known as pre-mRNA-splicing factor CWC26, belongs to the pre-mRNA retention and splicing (RES) complex. May also be involved in positioning the proximal bud pole signal . The presence of RES subunit homologues in numerous eukaryotes suggests that its function is evolutionarily conserved .
UV-stimulated scaffold protein A (UVSSA)
Type: Family

UV-stimulated scaffold protein A (UVSSA) is part of a UV-induced ubiquitinated protein complex involved in transcription-coupled nucleotide excision repair (TC-NER) in response to UV damage. It stabilise the TC-NER master organising protein ERCC6 (also known as CSB) by delivering the deubiquitinating enzyme USP7 to TC-NER complexes .
E3 UFM1-protein ligase 1 (Ufl1)
Type: Family

This entry represents E3 UFM1-protein ligase 1 (Ufl1).

The ubiquitin fold modifier 1 (Ufm1) is the most recently discovered ubiquitin-like modifier whose conjugation (ufmylation) system is conserved in multicellular organisms. Ufm1 is known to covalently attach with cellular protein(s) via a specific E1-activating enzyme (Uba5), an E2-conjugating enzyme (Ufc1), and a E3-ligating enzyme (Ufl1) . Ufl1 mediates the covalent attachment of the ubiquitin-like modifier Ufm1 to lysine residues on target proteins and plays a key role in reticulophagy (also called ER-phagy) induced in response to endoplasmic reticulum stress .
Nuclear speckle splicing regulatory protein 1, N-terminal (NSRP1_N)
Type: Domain

This domain is found at the N-terminal of Nuclear speckle splicing regulatory protein 1 (NRP1, also known as Nuclear speckle-related protein 70 and Coiled-coil domain-containing protein 55) and contains a coiled-coil domain that plays a critical role in NRP1 alternative splicing activity and self-oligomerization. NRP1 is a RNA-binding protein that mediates pre-mRNA alternative splicing regulation .
Ccdc97-like (Ccdc97-like)
Type: Family

This family includes coiled-coil domain-containing proteins of unknown function.
Keratinocyte-associated protein 2 (KRTCAP2)
Type: Family

Members of this family comprise various keratinocyte-associated proteins, including human Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit KCP2 (also known as Keratinocyte-associated protein 2), a subunit of the oligosaccharyl transferase complex that catalyses the initial in protein N-glycosylation .