SII-SWORD/CoKE huggingface dataset:
Protein of unknown function DUF2155 (DUF2155)
Type: Family

This entry contains various hypothetical prokaryotic proteins that have no known function.
Protein of unknown function DUF2158 (DUF2158)
Type: Family

This entry represents a family of predominantly prokaryotic proteins with no known function.
tRNA (guanine-N(1)-)-methyltransferase, C-terminal (RNA_MeTrfase_C_dom)
Type: Domain

This domain, found in various hypothetical prokaryotic proteins, has no known function. It is also found at the C-terminal of a few prokaryotic tRNA (guanine-N(1)-)-methyltransferases. It has a Rossmanoid fold, with a deep trefoil knot in its C-terminal region . Proteins of this family are members of the SPOUT (SpoU-TrmD) methyltransferase (MTase) superfamily, a large class of S-adenosyl-L-methionine (AdoMet or SAM)-dependent RNA MTases which are structurally characterised by a deep trefoil knot .
Protein of unknown function DUF2170 (DUF2170)
Type: Family

This entry represents a group of proteins from Proteobacteria, including Uncharacterized protein YjfI from Escherichia coli. Its function is unknown.
Protein of unknown function DUF2178, transmembrane (DUF2178_TM)
Type: Family

This entry, found in various hypothetical prokaryotic proteins, has no known function, but contains several predicted transmembrane helices.
Phosphatidate phosphatase APP1, catalytic domain (APP1_cat)
Type: Domain

This entry represents the catalytic domain of Phosphatidate phosphatase APP1 from yeast . This domain has a weak sequence similarity to the haloacid dehalogenase-like domain . APP1 catalyses the dephosphorylation of phosphatidate to yield diacylglycerol and may play a role in vesicular trafficking through its phosphatidate phosphatase activity at cortical actin patches .
Transcriptional regulator, AbiEi 2 antitoxin, Type IV TA system (AbiEi_2)
Type: Family

AbiEi_2 is the cognate antitoxin 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 included in the entry

.
Bacterial antitoxin of type II TA system, VapB (VapB_antitoxin)
Type: Family

VapB is the antitoxin of a bacterial toxin-antitoxin gene pair. The cognate toxin is VapC (

). The family contains several related antitoxins from Cyanobacteria and Actinobacterial families. Antitoxins of this class carry an N-terminal ribbon-helix-helix domain, RHH, that is highly conserved across all type II bacterial antitoxins, which dimerises with the RHH domain of a second VapB molecule. A hinge section follows the RHH, with an additional pair of flexible α helices at the C terminus. This C terminus is the Toxin-binding region of the dimer, and so is specific to the cognate toxin, whereas the RHH domain has the specific function of lying across the RNA-binding groove of the toxin dimer and inactivating the active-site - a more general function of all antitoxins .
Protein of unknown function DUF2196 (DUF2196)
Type: Family

A pair of adjacent genes, ablAB (acetyl-beta-lysine biosynthesis) encodes lysine 2,3-aminomutase and beta-lysine acetyltransferase in methanogenic archaea. Homologous pairs, possibly with identical function, occur in a wide range of species, including Bacillus subtilis. This model describes a conserved hypothetical protein, small in size, with a phylogenetic distribution moderately well correlated to that of the acetyltransferase family. This protein family is also described as DUF2196. The function is unknown.
Protein of unknown function DUF2197 (DUF2197)
Type: Family

This family represents various hypothetical bacterial proteins with no known function.
Protein of unknown function DUF2198 (DUF2198)
Type: Family

This entry represents a group of proteins from Bacilli, including Protein CsbA from Bacillus subtilis. This protein family has no known function.
Domain of unknown function DUF2202 (DUF2202)
Type: Domain

This domain is found in Uncharacterized protein MJ0754 from Methanocaldococcus jannaschii and similar proteins from bacteria and archaea. MJ0754 adopts a dimeric assembly, with each monomer consisting of six α-helices . It is a member of a broad superfamily of ferritin-like diiron-carboxylate proteins whose function is unknown. The conserved residues of a diiron centre are present within the putative active site.
Histidine kinase BarA, N-terminal (Histidine_kinase_BarA_N)
Type: Domain

This entry is found at the N terminus of various BarA-like signal transduction histidine kinases. These proteins are involved in the regulation of carbon metabolism via the csrA/csrB regulatory system . The role of this domain has not, as yet, been established.
Glucodextranase-like, C-terminal (Glucodextran_C)
Type: Domain

This entry represents the C-terminal domain of glucodextranase-like proteins found in various prokaryotic membrane-anchored proteins. It shows homology to the carbohydrate-binding unit of some glycosidases .
Protein of unknown function DUF2226 (DUF2226)
Type: Family

This entry includes hypothetical proteins of unknown function.
Protein of unknown function DUF2227, metal-binding (DUF2227_metal-bd)
Type: Family

This entry represents a family of hypothetical bacterial proteins that may possess metal binding properties; however, their exact function has not yet been determined.
Domain of unknown function DUF2231, transmembrane (DUF2231_TM)
Type: Domain

This domain, found in various hypothetical bacterial proteins, has no known function.
Protein of unknown function DUF2244, transmembrane (DUF2244_TM)
Type: Family

This entry consists of various bacterial putative membrane proteins with no known function.
Protein of unknown function DUF2250 (DUF2250)
Type: Family

Members of this family of hypothetical bacterial and archaeal proteins have no known function.
Histidine-specific methyltransferase, SAM-dependent (MeTrfase_dom)
Type: Domain

The mycobacterial members of this family are expressed from part of the ergothioneine biosynthetic gene cluster. EGTD is the histidine methyltransferase that transfers three methyl groups to the alpha-amino moiety of histidine, in the first stage of the production of this histidine betaine derivative that carries a thiol group attached to the C2 atom of an imidazole ring .
Mediator complex, subunit Med4 (Mediator_Med4)
Type: Family

The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins.

The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11.

Members of this family represent the Med4 subunit of the Mediator (Med) complex .
Domain of unknown function DUF2262 (DUF2262)
Type: Domain

This entry consists of various hypothetical bacterial proteins with no known function.
Microbial-type PARG, catalytic domain (PARG_cat_microbial)
Type: Domain

This entry represents the catalytic domain of the Poly(ADP-ribose) glycohydrolase (PARG) homologue predominantly found in bacteria and fungi. This enzyme hydrolyses the ribose-ribose bonds present in poly(ADP-ribose) (PAR) chains. Its structure shows a typical macro domain folding consisting of a seven-stranded β-sheet sandwiched between nine α-helices .
Domain of unknown function DUF2272 (DUF2272)
Type: Domain

This is a domain of unknown function found in proteins of unknown function predominantly found in bacteria.
Domain of unknown function DUF2179 (DUF2179)
Type: Domain

This entry, found mostly in hypothetical bacterial proteins, has no known function.
RNA transcription, translation and transport factor protein (RTRAF)
Type: Family

This entry represents RNA transcription, translation and transport factor protein (RTRAF, also known as hCLE/C14orf166) from eukaryotes. It is part of the DDX1-HSPC117-FAM98B complex that shuttles between the nucleus and the cytoplasm transporting RNAs . It is also a component of the tRNA-splicing ligase complex and is required for tRNA ligation . Human RTRAF works as a positive modulator of the RNA polymerase II activity . It also interacts with influenza virus polymerase subunit PA and plays an important role in influenza virus replication .
Small ribosomal subunit protein mS27 (Ribosomal_mS27)
Type: Family

This entry represents the small ribosomal subunit protein mS27 from animals, previously known as MRPS27. This protein binds to the mitochondrial 12S rRNA (12S mt-rRNA) and tRNA(Glu) . mS27 is involved also in positive regulation of cell proliferation and tumour cell growth .It is a pentatricopeptide repeat domain (PPR) protein required for mitochondrial protein synthesis .
CRISPR-associated protein Cas6, C-terminal (CRISPR-assoc_Cas6_C)
Type: Domain

The CRISPR-Cas system is a prokaryotic defence mechanism against foreign genetic elements. The key elements of this defence system are the Cas proteins and the CRISPR RNA.

Cas6 is a member of the RAMP (repeat-associated mysterious protein) superfamily . It is among the most widely distributed Cas proteins and is found in both bacteria and archaea . Cas6 functions in the generation of CRISPR-derived guide RNAs for invader defense in prokaryotes . The structure of this protein showed it adopts a tandem ferredoxin/RRM fold .

This entry represents a domain found in some CRISPR-associated proteins Cas6 and in uncharacterised proteins.
Protein of unknown function DUF2278 (DUF2278)
Type: Family

This entry consists of hypothetical proteins with no known function.
Biogenesis of lysosome-related organelles complex-1, subunit 2 (BLOC1_su2)
Type: Family

This entry represents a family of proteins that play a role in cellular proliferation, as well as in the biogenesis of specialised organelles of the endosomal-lysosomal system .
Protein of unknown function DUF2283 (DUF2283)
Type: Family

Members of this family of hypothetical proteins have no known function.
Protein of unknown function DUF2284, metal-binding (DUF2284_metal-binding)
Type: Family

This entry represents a family of predicted metal-binding bacterial and archaeal proteins with no known function.
Lunapark zinc ribbon domain (Lunapark_Znf)
Type: Domain

This domain, found mainly in the eukaryotic lunapark proteins, has no known function . It is predicted to fold into a structure typical for zinc ribbon domains. C. elegans lunapark-1, containing this domain, plays a role in synaptogenesis by regulating vesicular transport or localization .
Protein of unknown function DUF2301 (DUF2301)
Type: Family

This family contains uncharacterised integral membrane proteins.
Protein of unkown function DUF2303 (DUF2303)
Type: Family

Proteins in this entry are uncharacterised. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Protein of unknown function DUF2304 (DUF2304)
Type: Family

This entry represents hypothetical archaeal and bacterial proteins that have no known function.
DICT domain (DICT_dom)
Type: Domain

This domain is found associated with the catalytic domains of DIguanylate Cyclases and phosphodiesterases and Two-component systems (histidine kinase). It has therefore been termed the DICT domain. Secondary structure prediction suggests it assumes an α+β fold with a 4-stranded β-sheet. Based on the domain architectures in which it is found, the domain has been predicted to be involved in sensory function (including a role in light response, since it is found in photosynthetic bacteria and halophilic archaea). However, this has not been experimentally confirmed, and the domain also appears to occur in proteins for which there is no evidence of sensory function.
Glycoamylase-like, conserved domain (Glycoamylase-like_cons_dom)
Type: Domain

This domain adopts an α/α toroid fold, structurally similar to a number of glucoamylases (GH family 15 and 8 enzymes). This domain is also found in some hydrolases, such as ndvB from

family and members of the

family which includes beta-1,2-glucanases from Parabacteroides distasonis (also known as exo beta-1,2-glucooligosaccharide sophorohydrolase,

) and from Chitinophaga pinensis which hydrolyse linear beta-1,2-glucan (a polysaccharide from Gram-negative bacteria, with important roles in infection and symbiosis) .
Protein of unknown function DUF2330 (DUF2330)
Type: Family

Members of this family of hypothetical bacterial proteins have no known function.
Uncharacterized protein RP532 (RP532)
Type: Family

This entry consists of proteins from tailed bacteriophages (Caudovirales) and bacteria, including Uncharacterized protein RP532 from Rickettsia prowazekii (strain Madrid E). The characteristics of the protein distribution suggest prophage matches. Members of this family are thought to be membrane proteins.
Protein of unknown function DUF2336 (DUF2336)
Type: Family

Members of this family of hypothetical bacterial proteins have no known function.
Protein of unknown function DUF2339, transmembrane (DUF2339_TM)
Type: Family

This entry, found in various hypothetical bacterial proteins, has no known function.
Holliday junction resolvase-related domain (Hday_junct_resolvase-rel_dom)
Type: Domain

This domain is found in various predicted bacterial endonucleases which are distantly related to archaeal Holliday junction resolvases.
Predicted 3'-5' exonuclease, PolB-like (3'-5'_exonuclease_PolB-like)
Type: Domain

This entry represents various prokaryotic 3'-5' exonucleases and hypothetical proteins.
Tail assembly protein E/E' (Phage_tail_E/E')
Type: Family

This entry includes a set of bacteriophage proteins, Tail assembly protein E and E', also known as TAC (tail assembly chaperone) which promote tail assembly by creating a scaffold for the tail tube proteins. Tail assembly proteins E and E' would wrap the linear tape measure protein to create a tail assembly scaffold .
Glycosyltransferase 2-like, prokaryotic type (GlycosylTrfase-like_prok)
Type: Domain

This entry represetns a predicted glycosyltransferase domain found in a set of prokaryotic proteins that includes putative glucosyltransferases involved in bacterial capsule biosynthesis .
Host attachment protein (Host_attachment_protein)
Type: Family

Members of this family of bacterial proteins are required for the attachment of the bacterium to host cells .
Type IV methyl-directed restriction enzyme EcoKMcrBC (McrC)
Type: Family

Members of this family of prokaryotic endonucleases modify the specificity of McrB restriction by expanding the range of modified sequences that are restricted . It does not bind DNA. Type IV methyl-directed restriction enzyme EcoKMcrBC (McrC) adopts a dimeric configuration while free and form tetradecamers of 12 McrB and 2 McrC protomers when bound to this protein .
Thiamine-phosphate synthase ThiN (ThiN)
Type: Domain

Thiamine-phosphate synthase ThiN condenses 4-methyl-5-(beta-hydroxyethyl)thiazole monophosphate (THZ-P) and 4-amino-5-hydroxymethyl pyrimidine pyrophosphate (HMP-PP) to form thiamine monophosphate (TMP) . This enzyme is sometimes part of a bifunctional thiamine biosynthesis protein which also includes ThiD (a hydroxymethylpyrimidine/phosphomethylpyrimidine kinase) .

This domain is also present in the transcriptional repressor ThiR from Haloferax volcanii (

), which is catalytically inactive as it lacks the conserved Met residue found in the extended α-helix near the active site His in ThiN . Moreover, it was shown that thiamine biosynthesis in archaea is regulated by ThiR and not by a riboswitch.
Translational regulator Com (Translation_reg_Com)
Type: Family

Com is a bacteriophage protein that acts as a translational regulator of the DNA modification protein Mom . Binding of Com to the translation intitation region of the mom gene causes a conformational change that is thought to enhancing ribosome binding .
Uncharacterised protein family, nitrogen regulatory protein PII-related (Unchr_N-regulatory-PII-rel)
Type: Family

This family of hypothetical archaeal proteins has no known function. They are distantly similar to the nitrogen regulatory protein PII.
CO dehydrogenase accessory protein CooT (CooT)
Type: Family

CooT is an accessory protein required for maturation of Carbon Monoxide Dehydrogenase (CODH). It is a member of a Ni(ii)-binding protein family, linked to anaerobic metabolism in bacteria and archaea, and in most cases to the presence of CODH. Structure analysis indicates that it is a homodimer featuring a fold that resembles an Sm-like domain .
Flagellar protein FlgJ, N-terminal (Flagellar_prot_FlgJ_N)
Type: Domain

The N-terminal domain of the FlgJ protein is directly involved in flagellar rod assembly, while the adjacent C-terminal domain is a flagellum-specific muramidase (peptidoglycan hydrolase) required for formation of the outer membrane L ring .
CD-NTase-associated protein 12/Pycsar effector protein, TIR domain (CAP12/PCTIR_TIR_dom)
Type: Domain

This entry represents a TIR domain found in prokaryotic nucleotide-binding proteins, including CD-NTase-associated protein 12 (CAP12) and Pycsar effector proteins (

). Members of this entry are part of anti phage resistance systems that provide immunity against bacteriophage. CAP12 is part of the CBASS (cyclic oligonucleotide-based antiphage signaling system) and binds c-di-GMP and 3'-3'-cGAMP, cyclic nucleotides synthesized by the CD-NTase protein in response to infection that serve as specific second messenger signals to activate a diverse range of effectors, leading to bacterial cell death and thus abortive phage infection . Pycsar effector proteins are part of the Pycsar (pyrimidine cyclase system for anti phage resistance) and are activated by cyclic nucleotides produced by the pyrimidine cyclase (PycC) in response to infection. The TIR effector domain oligomerizes and functions as NADase that deplete the cell of NAD+.
vWA found in TerF C terminus (vWA_TerF_C)
Type: Domain

vWA domain fused to TerD domain typified by the TerF protein . Sometimes it is found as solos.
Uncharacterised protein family Smp (Uncharacterised_Smp)
Type: Family

This entry represents a group of bacterial proteins that are membrane proteins that effect the expression of haemolysin under anaerobic conditions .
Transmembrane protein 231 (TMEM231)
Type: Family

The proteins in this entry belong to transmembrane protein family 231; they have no known function.
RNA-binding protein AU-1/Ribonuclease E/G (RNA-bd_AU-1/RNase_E/G)
Type: Domain

This entry represents ribonuclease E/G and RNA-binding protein AU-1.

Ribonuclease E and ribonuclease G are related enzymes that cleave a wide variety of RNAs . RNA-binding protein AU-1 binds to RNA loop regions that are with AU-rich sequences .
Transmembrane protein 214 (TMEM214)
Type: Family

TMEM214 is a critical mediator, in cooperation with CASP4, of endoplasmic reticulum-stress induced apoptosis. It is required or the activation of CASP4 following endoplasmic reticulum stress .
WASH complex subunit 3 (WASHC3)
Type: Family

The WASH (WASP and Scar homologue) complex is present at the surface of endosomes and recruits and activates the Arp2/3 complex to induce mediated actin nucleation. The WASH complex plays a key role in the fission of tubules that serve as transport intermediates during endosome sorting .

The WASH complex consists of several subunits: F-actin-capping protein subunit alpha (CAPZA1, CAPZA2 or CAPZA3), F-actin-capping protein subunit beta (CAPZB), WASH (WASH1, WASH2P, WASH3P, WASH4P, WASH5P or WASH6P), FAM21 (FAM21A, FAM21B or FAM21C), KIAA1033, KIAA0196 (strumpellin) and CCDC53.

This entry represents the WASH complex subunit 3, also known as CCDC53.
rRNA-processing protein Efg1 (Efg1)
Type: Family

This entry represents the rRNA-processing protein Efg1 family. Efg1 is involved in rRNA processing .
Ferry endosomal RAB5 effector complex subunit 3 (Fy-3)
Type: Family

This entry represents a human Ferry endosomal RAB5 effector complex subunit 3 (Fy-3) and similar sequences from animals and some fungal species.
Fy-3 is a component of the FERRY complex (Five-subunit Endosomal Rab5 and RNA/ribosome intermediary), which directly interacts with mRNAs and RAB5A, and functions as a RAB5A effector involved in the localisation and the distribution of specific mRNAs most likely by mediating their endosomal transport. The complex recruits mRNAs and ribosomes to early endosomes through direct mRNA-interaction .
This family was previously known as DUF2362.
CCR4-NOT transcription complex subunit 11 (CNOT11)
Type: Family

The CCR4-NOT complex plays a key role in mRNA decay in all eukaryotes, thereby contributing importantly to gene expression regulation . Human C2ORF29 proteins, also known as CNOT11, is a component of the CCR4-NOT complex. CNOT11 interacts with the first amino acids of CNOT1 and with CNOT10 and is required for the association of CNOT10 with the CCR4-NOT complex .
Mediator complex, subunit Med17 (Mediator_Med17)
Type: Family

The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins.

The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11.

This entry represents subunit Med17 of the Mediator complex. The Med17 subunit is located within the head domain and is essential for cell viability to the extent that a mutant strain of Saccharomyces cerevisiae (Baker's yeast) lacking it shows all RNA polymerase II-dependent transcription ceasing at non-permissive temperatures.
BLOC-1-related complex subunit 6 (BORCS6)
Type: Family

BORC is a multisubunit complex that regulates the positioning of lysosomes at the cell periphery, and consequently affects cell migration. BORC associates with the lysosomal membrane, where it functions to recruit the small GTPase Arl8. This initiates a series of interactions that promote the microtubule-guided transport of lysosomes toward the cell periphery .

The BORC complex consists of 8 subunits. This family represents subunit 6.