SII-SWORD/CoKE huggingface dataset:
Alpha C protein, N-terminal (AlphaC_N)
Type: Domain

The alpha C protein (ACP) is found in Streptococcus and acts as an invasin which plays a role in the internalisation and translocation of the organism across human epithelial surfaces. Group B Streptococcus is the leading cause of diseases including bacterial pneumonia, sepsis and meningitis. The N-terminal of ACP is associated with virulence and forms a β sandwich and a three helix bundle .
Protein of unknown function DUF1806 (DUF1806)
Type: Family

This entry consists of bacterial uncharacterised proteins. The structure of one of the proteins has been solved and it adopts a β barrel-like structure.
Nuclear receptor coactivator, receptor-binding domain (SRC/p160_LXXLL)
Type: Domain

This domain is found in steroid/nuclear receptor coactivators and contains two LXXLL motifs that are involved in receptor binding and includes SRC-1/NcoA-1, NcoA-2/TIF2, pCIP/ACTR/GRIP-1/AIB1 .
Axin beta-catenin binding (Axin_b-cat-bd)
Type: Domain

Proteins in this entry are found on the scaffolding protein Axin which is a component of the beta-catenin destruction complex. It competes with the tumour suppressor adenomatous polyposis coli protein (APC) for binding to beta-catenin .
Protein of unknown function DUF1810 (DUF1810)
Type: Family

This is a family of uncharacterised proteins. The structure of one of the members in this family, Rv1873 from Mycobacterium tuberculosis (

), has been solved and it adopts a mainly α-helical structure .
YfhH-like (YfhH-like)
Type: Family

This entry consists of a group of proteins predominantly found in Firmicutes, including Uncharacterized protein YfhH from Bacillus subtilis and protein GK0453 from Geobacillus kaustophilus. GK0453 shows two small domains: an helix-turn-helix like motif is found in its N-terminal domain while an SH3-like β-barrel like structure is observed its C-terminal region. Its specific function is unknown . Some of the members of this protein family are annotated as being transcriptional regulators (see

,

).
CDT1 Geminin-binding domain-like (CDT1_Gemini-bd-like)
Type: Domain

This entry represents the geminin-binding domain of the DNA replication factor CDT1 and related domains whose functions are not known .
BAAT/Acyl-CoA thioester hydrolase C-terminal (BAAT_C)
Type: Domain

Acyl-CoA thioesterases are a group of enzymes that catalyse the hydrolysis of acyl-CoAs to the free fatty acid and coenzyme A (CoASH), providing the potential to regulate intracellular levels of acyl-CoAs, free fatty acids and CoASH. Bile acid-CoA:amino acid N-acetyltransferase (BAAT) is involved in bile acid metabolism and may also act as an acyl-CoA thioesterase that regulates intracellular levels of free fatty acids .

This entry represents a catalytic domain is found at the C terminus of acyl-CoA thioester hydrolases and bile acid-CoA:amino acid N-acetyltransferases.
Fimbrium subunit FimB/Mfa2/Mfa3 (FimB/Mfa2/Mfa3)
Type: Family

Many Bacteroides-like bacterial species, including Porphyromonas gingivalis, the causal agent of periodontal infection, carry at least two types of fimbriae, namely FimA and Mfa1 fimbriae, following the names of their major subunit proteins . Normally, FimA fimbriae are long filaments that are easily detached from cells, whereas Mfa1 fimbriae are short filaments that are tightly bound to cells.

In many bacteria, the gene encoding the major fimbrilin typically forms a cluster with several additional genes encoding fimbrial minor components. FimB, the product of the gene immediately downstream of the fimA gene, regulates the length and expression of FimA fimbriae. Additionally, FimB functions as an anchor of the fimbriae . Similarly, Mfa2 seems to regulate the length and attachment of Mfa1 fimbriae. Mfa2 and Mfa1 are associated with each other in whole P. gingivalis cells to the extent that Mfa2 is located on the cell surface and probably associated with Mfa1 fimbriae in such a way that it anchors the Mfa1 fimbriae to the cell surface and regulates Mfa1 filament length . Mfa3 is a tip protein of the Mfa1 fimbriae that may function in the integration of accessory proteins and in the colonization of P. gingivalis .

.
Nucleotidyl transferase AbiEii toxin, Type IV TA system (AbiEii)
Type: Family

This family was recently identified as belonging to the nucleotidyltransferase superfamily . AbiEii is the cognate toxin of the type IV toxin-antitoxin 'innate immunity' bacterial abortive infection (Abi) system that protects bacteria from the spread of a phage infection. The Abi system is activated upon infection with phage to abort the cell thus preventing the spread of phage through viral replication. There are some 20 or more Abis, and they are predominantly plasmid-encoded lactococcal systems. TA, toxin-antitoxin, systems on plasmids function by killing cells that lose the plasmid upon division. AbiE phage resistance systems function as novel Type IV TAs and are widespread in bacteria and archaea. The cognate antitoxin is

.
Protein of unknown function DUF1815 (DUF1815)
Type: Family

This entry is about 100 amino acids in length and is functionally uncharacterised.
Toxin SymE-like (Toxin_SymE-like)
Type: Domain

SymE (SOS-induced yjiW gene with similarity to MazE) is an SOS-induced toxin. It inhibits cell growth, decreases protein synthesis and increases RNA degradation. It may play a role in the recycling of RNAs damaged under SOS response-inducing conditions. Its translation is repressed by the antisense RNA SymR, which acts as an antitoxin .

SymE belongs to type I toxin-antitoxin systems, but it does not show functional homology to other type I toxin proteins. Its function resembles that of type II toxins such as MazF, which can cleave mRNA independent of the ribosome. However, SymE has homology to the AbrB-fold superfamily proteins such as MazE, which act as transcriptional factors and antitoxins in various type II TA modules . It seems probable that SymE has evolved into an RNA cleavage protein with toxin-like properties from a transcription factor or antitoxin .
Protein of unknown function DUF1816 (DUF1816)
Type: Family

is associated with the

domain suggesting this protein could have a role in phycobilisomes.
Protein chlororespiratory reduction 6 (CRR6)
Type: Family

Chlororespiratory reduction 6 is a factor required for the assembly or stabilisation of the chloroplast NAD(P)H dehydrogenase complex in Arabidopsis .
Protein of unknown function DUF1818 (DUF1818)
Type: Family

This entry represents a small family of uncharacterised cyanobacterial proteins.
BrxA (BrxA)
Type: Family

BrxA is part of the phage resistance system BREX (Bacteriophage Exclusion). It shares structural homology with the RNA-binding antitermination protein NusB .
Protein of unknown function DUF1820 (DUF1820)
Type: Family

This protein includes small functionally uncharacterised proteins of around 100 amino acids in length.
Protein of unknown function DUF1822 (DUF1822)
Type: Family

This entry includes cyanobacterial proteins of unknown function.
Protein of unknown function DUF1823 (DUF1823)
Type: Family

These proteins are functionally uncharacterised.
Protein of unknown function DUF1824 (DUF1824)
Type: Family

This uncharacterised group of proteins are principally found in cyanobacteria.
Protein of unknown function DUF1825 (DUF1825)
Type: Family

These roteins are uncharacterised and are principally found in cyanobacteria.
Protein of unknown function DUF1826 (DUF1826)
Type: Family

These proteins are functionally uncharacterised.
Putative ParB-like nuclease (ParBc_2)
Type: Family

These proteins are probably distantly related to

. Suggesting these, uncharacterised proteins have a nuclease function.
IDEAL domain (IDEAL_dom)
Type: Domain

This short domain is found at the C terminus of proteins in the UPF0302 family. The domain is named after the sequence of the most conserved region in some members. The function of this domain is unknown.
DGC (DGC)
Type: Family

This protein appears to be a zinc binding domain from the conservation of four potential chelating cysteines. The protein is named after a conserved central motif, the function is unknown.

The anaerobic and virulence modulator AnvM is found in a wide range of bacteria and contains a DGC conservative sequence. AnvM functions as a regulator controlling multiple cellular functions and the interaction between bacteria and host immune systems .
Protein of unknown function DUF1827 (DUF1827)
Type: Family

This presumed domain has no known function.
Domain of unknown function DUF1828 (DUF1828)
Type: Domain

This domain is functionally uncharacterised.
Domain of unknown function DUF1829 (DUF1829)
Type: Domain

This short protein is usually associated with

.
YolD-like protein (YolD)
Type: Family

These proteins are functionally uncharacterised. However it has been predicted that these proteins are functionally equivalent to the UmuD subunit of polymerase V from Gram-negative bacteria .
Uncharacterised domain UPF0302, N-terminal (UPF0302_N)
Type: Domain

These proteins are functionally uncharacterised.
Protein of unknown function DUF1830 (DUF1830)
Type: Family

This group of short proteins is functionally uncharacterised.
Putative amino acid metabolism (Amino_acid_metab_prot_put)
Type: Family

Solution of the structure of the Lactobacillus plantarum protein from this family has indicated a potential new fold with remote similarities to TBP-like (TATA-binding protein) structures. This similarity, in combination with genomic context analysis, leads us to propose an involvement in amino-acid metabolism. The potentially novel fold is an α + β fold comprising two β sheets packed against a single helix . The enzyme is present in the cytosol.
FRG domain (FRG-dom)
Type: Domain

This entry contains a conserved N-terminal (F/Y)RG motif. It is functionally uncharacterised.
Uncharacterised protein family, YugN-like (Uncharacterised_YugN-like)
Type: Family

This entry contains proteins related to Bacillus subtilis YugN, they are functionally uncharacterised.
XisI protein (XisI)
Type: Family

This family contains XisI proteins, also known as FdxN element excision controlling factors, and similar proteins. FdxN element is excised from the chromosome during heterocyst differentiation in cyanobacteria. This is accomplished by the large serine recombinase XisF (fdxN element site-specific recombinase). The xisH as well as the xisF and xisI genes are required. XisI may function as recombination directionality factor (RDF), and needs XisH which may function as an endonuclease .
DNA sulphur modification protein DndE (DNA_S_DndE)
Type: Family

This entry describes the DndE protein encoded by an operon associated with a sulphur-containing modification to DNA (phosphorothioation). The operon is sporadically distributed in bacteria, much like some restriction enzyme operons. DndE is part of a protein complex that also includes IscS, DndC, and DndE, involved in phosphorothioation (PT) . DndE binds to DNA in vitro, with a preference for nicked dsDNA , but its nicked dsDNA-binding capacity does not seem essential for PT modification .
KGK (KGK)
Type: Family

This protein is found in one or two copies in cyanobacterial proteins. It is named after a short sequence motif.
Bacteriophage Mu, Gp37 (Phage_Mu_Gp37)
Type: Family

This entry is represented by Bacteriophage Mu, Gp37 (also known as Probable tail terminator protein) which may stop tail tube polymerisation by capping the rapidly polymerising tail tube once it has reached its requisite length and prevents its depolymerisation . This family also has prophages matches, such as the Gp37 protein from the FluMu prophage.
Domain of unknown function DUF1835 (DUF1835)
Type: Domain

This is a presumed domain found in functionally uncharacterised proteins from bacteria. It is found associated with

at the C-terminal.
Protein of unknown function DUF1833 (DUF1833)
Type: Family

This family of proteins are functionally uncharacterised and are predicted to adopt an all-β fold . They are often found in gene neighbourhoods containing genes for an NlpC peptidase and a Ubiquitin domain predicted to be involved in tail assembly .
Protein of unknown function DUF1836 (DUF1836)
Type: Family

This protein family appears to be primarily involved in transcriptional regulation and cellular processes. Members of this family, such as the one represented by

(gene gbs1388), exhibit high levels of transcriptional activity and may be regulated by factors like the rex gene, indicating a role in significant cellular processes . Another member,

(gene name cbei_4884), is implicated in strain degeneration and regulatory functions linked to sporulation and solvent formation in Clostridium beijerinckii, suggesting conservation among clostridial species . The sgo_1308 gene encodes a protein (

) containing the DUF1836 domain, which belongs to the helix-turn-helix (HTH) clan, hinting at its role in transcriptional regulation, specifically influencing bacterial hemolysins III . Overall, this protein family is characterised by domain structures that suggest roles in DNA binding and regulatory functions across various bacterial species.
Anti-bacteriophage protein A/HamA, C-terminal domain (AbpA_HamA_C)
Type: Domain

Hachiman antiphage defense system has been described in Ralstonia solanacearum species complex (RSSC) and in Escherichia coli, and is composed of two genes, hamAB, which encode Anti-bacteriophage protein A (also known as HamA, represented in this entry), and an helicase (HamB/AbpB). These proteins confer temperature dependent resistance to phages T2, T4, T7 and lambda but not RB32 or RB69 .

This entry represents a domain found at the C-terminal of AbpA and in similar proteins predominantly from bacteria.
WRC domain (WRC_dom)
Type: Domain

The plant GROWTH-REGULATING FACTOR (GRF) proteins are putative transcription factors. They contain one or two WRC (Trp, Arg, Cys) domain(s). The WRC domain has two distinctive structural features, namely many basic amino acids (Arg and Lys) and the conserved spacing of three Cys and one His residues, the C3H motif. The basic amino acids are highly conserved, indicating that they are essential for the function of the WRC domain, probably as nuclear localization signal. The C3H motif is also absolutely conserved and may mediate binding to DNA .
Glutamine-Leucine-Glutamine, QLQ (Gln-Leu-Gln_QLQ)
Type: Domain

The QLQ domain is characterised by the conserved Gln-Leu-Gln residues. Another feature of this domain is the absolute conservation of bulky aromatic/hydrophobic and acidic amino acid residues such as Phe, Trp, Tyr, Leu, Glu, or their equivalents in terms of chemical and radial properties. The Pro residue is also absolutely conserved. These amino acid residues are critical for the function of the QLQ domain, probably for protein-protein interaction .

Some proteins known to conatin a QLQ domain are listed below:

Plant GROWTH-REGULATING FACTOR (GRF) proteins, putative transcription factors.

Eukaryotic SWI2/SNF2, transcriptional coactivators.
Dopa 4,5-dioxygenase (DOPA_dioxygen)
Type: Family

This family of proteins includes

, a DOPA 4,5-dioxygenase that is involved in synthesis of betalain . It converts 3,4-dihydroxyphenylalanine to betalamic acid, a yellow chromophore.
Flagellin D3 (Flagellin_D3)
Type: Domain

This domain is found in the central portion bacterial flagellin FliC, it contains a structural motif called a β-folium fold . Although no specific function is assigned its deletion leads to a reduction in filament stability .
GSCFA (GSCFA)
Type: Domain

This group of proteins are functionally uncharacterised. They have been named GSCFA after a highly conserved N-terminal motif in the alignment, they are functionally uncharacterised.
GAD-related (GAD-rel)
Type: Domain

This entry represents the N-terminal domain of the type VI secretion system (T6SS) immunity protein Tdi1 from Agrobacterium tumefaciens (Atu4351,

) and other bacterial proteins. This domain, which appears to be distantly related to the GAD domain

, folds into a a seven-stranded twisted antiparallel β-sheet, a two-stranded antiparallel β-sheet, and six helices. There is a positive groove that extends to the C-terminal domain (

, which may exist as an insertion), likely to play a role in nucleotide binding .
HopJ type III effector protein (HopJ)
Type: Family

Pathovars of Pseudomonas syringae interact with their plant hosts via the action of Hrp outer protein (Hop) effector proteins, injected into plant cells by the type III secretion system. The proteins are called HopJ after the original member HopPmaJ .
WbqC-like protein family (WbqC)
Type: Family

This family of proteins are functionally uncharacterised. However, it is found in an O-antigen gene cluster in Escherichia coli and other bacteria suggesting a role in O-antigen production. It has been suggested that wbnG may code for a glycine transferase .
Phage-like element PBSX protein XkdN-like (XkdN-like)
Type: Family

This entry is represents Phage-like element PBSX protein XkdN from Bacillus subtilis (strain 168) and similar proteins predominantly found in Firmicutes and some tailed bacteriophages. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. Members of this group of proteins are chaperones involved in phage tail assembly and have been predicted to form a spiral structure .
Uncharacterised protein family YfcL (UPF_YfcL)
Type: Family

This group of proteins are functionally uncharacterised. They are related to the short YfcL protein from Escherichia coli.
Uncharacterised protein family, YqcI/YcgG (Uncharacterised_YqcI/YcgG)
Type: Family

This group of proteins are functionally uncharacterised. They include YqcI and YcgG from Bacillus subtilis. The alignment contains a conserved FPC motif at the N terminus and CPF at the C terminus.
Protein of unknown function DUF1839 (DUF1839)
Type: Family

This family of proteins are functionally uncharacterised.
Protein of unknown function DUF1838 (DUF1838)
Type: Family

This family of proteins are functionally uncharacterised. According to structure predictions, they may adopt a β-barrel fold. This entry includes proteins mainly from bacteria but also a few fungal and lower eukaryotes species.
Protein of unknown function DUF1840 (DUF1840)
Type: Family

This family of proteins are functionally uncharacterised.
Domain of unknown function DUF1842 (DUF1842)
Type: Domain

This domain is found at the N terminus of proteins that are functionally uncharacterised.
Protein of unknown function DUF1841 (DUF1841)
Type: Family

This family of proteins are functionally uncharacterised.
Domain of unknown function DUF1843 (DUF1843)
Type: Domain

This domain is found in functionally uncharacterised proteins. It can be found independently or at the C terminus of the protein.
Protein of unknown function DUF1844 (DUF1844)
Type: Family

This family of proteins are functionally uncharacterised.
Transcriptional regulator AcaB (AcaB)
Type: Family

This family of proteins is found in the IncC family of broad-host-range plasmids which enables the spread of antibiotic resistance genes among human enteric pathogens. Recently, AcaB member has been characterised as a transcriptional regulator that plays a crucial role in the regulation of IncC conjugation. It is a DNA binding protein which binds upstream of the acaDB promoter to increase its transcription and, in turn, acaDB activates the transcription of IncC conjugation genes. Structurally, AcaB consists of two helical hairpins in tandem which assemble into an anti-parallel four-helix bundle to form a two-stranded antiparallel β-sheet positioned parallel to the helices. This is structurally similar to bacterial transcription factors from the ribbon-helix-helix (RHH) superfamily .
Protein of unknown function DUF1847 (DUF1847)
Type: Family

This group of proteins are functionally uncharacterised. They contain 4 N-terminal cysteines that may form a zinc-binding domain.
Protein of unknown function DUF1848 (DUF1848)
Type: Family

This group of proteins are functionally uncharacterised. The C terminus contains a cluster of cysteines that are similar to the iron-sulphur cluster found at the N terminus of

.
Family of unknown function DUF1846 (DUF1846)
Type: Family

This entry represents the uncharacterised protein family DUF1846 (also kwon as UPF0371). Some members of the family are annotated as ATP-dependent peptidases. This is a P-loop-like domain

.
EipB-like (EipB-like)
Type: Family

This entry includes a group of bacterial proteins, including EipB from Brucella. EipB is a periplasmic protein that functions as part of a system required for cell envelope homeostasis. It adopts a β-spiral fold, consisting of 14 β-strands and 2 α-helices .
Protein of unknown function DUF1850 (DUF1850)
Type: Family

This entry contains proteins, which are functionally uncharacterised. Some members of this family appear to be miss-annotated as RocC an amino acid transporter from Bacillus subtilis.
T6SS immunity protein Tdi1, C-terminal (T6SS_Tdi1_C)
Type: Domain

This entry represents a domain found at the C-terminal region of the type VI secretion system (T6SS) immunity protein Tdi1 from Agrobacterium tumefaciens (Atu4351,

) and similar bacterial proteins. Tdi1 is organised into a N-terminal GAD-related domain (

) and a C-terminal domain likely to exist as an insertion in the GAD-like domain. This domain, previously known as DUF1851, shows a two-stranded antiparallel β-sheet and four helices. A positive groove that extends to both domains may be associated with nucleotide binding .
Protein of unknown function DUF1853 (DUF1853)
Type: Family

This family of proteins are functionally uncharacterised.
MesX (MesX)
Type: Family

This family represents the putative oxygenase component of the oxygen-dependent methionine synthase MesD, called MesX, present in aerobic bacteria . MesX is required for MesD for its activity. MesD/MesX has the advantage of not requiring cobalamin for methionine synthesis.
Domain of unknown function DUF1854 (DUF1854)
Type: Domain

These protein is functionally uncharacterised. It is found at the C terminus of a number of ATP transporter proteins suggesting it may be involved in ligand binding.
Nuclear pore complex, NUP2/50/61 (NUP2/50/61)
Type: Domain

This entry represents a domain found in Nup2, 50 and 61, which are components of the nuclear pore complex.

NUP2 encodes a non-essential nuclear pore protein that has a central domain similar to those of Nsp1 and Nup1. Transport of macromolecules between the nucleus and the cytoplasm of eukaryotic cells occurs through the nuclear pore complex (NPC), a large macromolecular complex that spans the nuclear envelope . The structure of the vertebrate NPC has been studied extensively; recent reviews include . The yeast NPC shares several features with the vertebrate NPC, despite being smaller and less elaborate . Many yeast nuclear pore proteins, or nucleoporins, have been identified by a variety of genetic approaches . nup2 mutants show genetic interactions with nsp1 and nup1 conditional alleles . Nup1 interacts with the nuclear import factor Srp1 and with the small GTPase Ran (encoded by GSP1) .
ROCK, Rho binding domain (ROCK_Rho-bd_dom)
Type: Domain

The Rho-ROCK pathway modulates the phosphorylation level of a variety of important signalling proteins and is thereby involved in miscellaneous cellular processes including cell migration, neurite outgrowth, and smooth muscle contraction. The enzyme activity of the two ROCK isoforms, ROCKI/ ROKbeta/p160(ROCK) and ROCKII/ROKalpha/Rho kinase, is auto-inhibited in the free state but is activated through direct binding to the small GTPase Rho in the GTP-bound form.
Vinculin-binding site-containing domain (Vinculin-bd_dom)
Type: Domain

Vinculin binding sites are predominantly found in talin and talin-like molecules, enabling binding of vinculin to talin, stabilising integrin-mediated cell-matrix junctions . Talin, in turn, links integrins to the actin cytoskeleton. The consensus sequence for Vinculin binding sites is LxxAAxxVAxxVxxLIxxA, with a secondary structure prediction of four amphipathic helices. The hydrophobic residues that define the VBS are themselves 'masked' and are buried in the core of a series of helical bundles that make up the talin rod .