SII-SWORD/CoKE huggingface dataset:
30K viral movement protein, C-terminal (30K_MP_C)
Type: Domain

This entry represents the C-terminal region found in viral movement proteins (MP) of the 30K type. This region has been suggested to be conserved in secondary structure in Ophioviruses Mps. It contains two parts, (i) a long segment with the potential to form an α-helix (alphaB), rich in charged residues, and (ii) a region highly variable in sequence downstream of alphaB.

The C-terminal region corresponds to the protease domain which contains a strictly conserved DTG tripeptide, also found in related aspartic retroviral proteases. This protease is required for autocleavage of the Movement Protein of ophioviruses in an N-terminal part that supports movement of viral particles through the plant, and this C-terminal part which retains protease activity . contains a strictly conserved DTG tripeptide which is probably conserved for functional, rather than structural reasons. Mutations in the aspartate residue in the core domain had an impact on cell to cell movement .
Probable zinc-ribbon domain, plant (Zinc_ribbon_12)
Type: Domain

This eukaryotic domain has no known function.
Protein of unknown function DUF3134 (DUF3134)
Type: Family

This family of proteins with unknown function are mostly from Cyanobacteria.
Protein of unknown function DUF3135 (DUF3135)
Type: Family

This family of proteins with unkown function appears to be restricted to Proteobacteria.
Protein of unknown function DUF3136 (DUF3136)
Type: Family

This family of proteins with unknown function appear to be restricted to Cyanobacteria.
Protein of unknown function DUF3137 (DUF3137)
Type: Family

This bacterial family of proteins has no known function.
Protein of unknown function DUF3138 (DUF3138)
Type: Family

This family of proteins with unknown function appear to be restricted to Proteobacteria.
Protein of unknown function DUF3139 (DUF3139)
Type: Family

This family of proteins with unknown function appears to be restricted to Firmicutes.
Protein of unknown function DUF3140 (DUF3140)
Type: Family

Some members in this family of proteins are annotated as DNA binding proteins. No function is currently known.
Protein of unknown function DUF3142 (DUF3142)
Type: Family

This bacterial family of proteins has no known function.
Protein of unknown function DUF3143 (DUF3143)
Type: Family

This family of proteins has no known function.
Protein of unknown function DUF3144 (DUF3144)
Type: Family

This family of proteins with unknown function appears to be mainly restricted to Proteobacteria.
Protein of unknown function DUF3145 (DUF3145)
Type: Family

This family of proteins with unknown function appear to be restricted to Actinobacteria.
Protein of unknown function DUF3146 (DUF3146)
Type: Family

This family of proteins with unknown function appear to be restricted to Cyanobacteria.
Protein of unknown function DUF3147 (DUF3147)
Type: Family

Some members in this family of proteins are annotated as membrane proteins however this cannot be confirmed. Currently no function is known.
Protein of unknown function DUF3149 (DUF3149)
Type: Family

This bacterial family of proteins has no known function.
Protein CHLORORESPIRATORY REDUCTION 42-like (CRR42-like)
Type: Family

This family includes includes Protein CHLORORESPIRATORY REDUCTION 42 (CRR42) from Arabidopsis thaliana, which is required for both formation and activity of the chloroplast NAD(P)H dehydrogenase (NDH) complex of the photosynthetic electron transport chain . CRR42 functions in assembly or stabilization of the NDH complex and it is likely involved, together with CRR1 and CRR6, in the incorporation of NdhJ, NdhM, NdhK and NdhI into the NDH subcomplex A assembly intermediate (NAI500) to produce the complex NAI400 . This family also includes uncharacterised proteins from cyanobacteria.
Protein of unknown function DUF3150 (DUF3150)
Type: Family

This bacterial family of proteins with unknown function appears to be restricted to Proteobacteria.
Holin of 3TMs, for gene-transfer release (GTA_holin_3TM)
Type: Family

This is a family of bacterial 3TM holins. In Rhodobacter capsulatus the protein is expressed just overlapping and downstream of a putative N-acetylmuramidase lysozyme (an endolysin) thought to be responsible for lysing a phage particle, RcGTA - a gene-transfer agent. A holin would be necessary for such an endolysin to access the peptidoglycan . Gene-transfer agents are bacteriophage-like genetic elements with the sole known function of horizontal gene transfer, serving an important role in microbial evolution. In order to be released from the cell these require the combined action of an endolysin and this holin .
Protein of unknown function DUF3155 (DUF3155)
Type: Family

This family of proteins with unknown function are mostly from Cyanobacteria.
Protein of unknown function DUF3153 (DUF3153)
Type: Family

This family of proteins with unknown function are found in Bacteria.
Protein of unknown function DUF3156 (DUF3156)
Type: Family

This family of proteins with unknown function appears to be restricted to Proteobacteria.
Protein of unknown function DUF3157 (DUF3157)
Type: Family

This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.
Protein of unknown function DUF3158 (DUF3158)
Type: Family

Some members in this family of proteins are annotated as integrase regulator R however this cannot be confirmed. This family of proteins with unknown function appear to be restricted to Proteobacteria.
Protein of unknown function DUF3110 (DUF3110)
Type: Family

This family of proteins has no known function.
Bacteriophage B3, Orf6 (Phage_B3_Orf6)
Type: Family

This entry is represented by Bacteriophage B3, Orf6. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Protein of unknown function DUF3165 (DUF3165)
Type: Family

Some members in this family of proteins are annotated as membrane proteins however this cannot be confirmed. Currently there is no known function.
Tail completion protein gp17 (Gp17-like)
Type: Family

Gp17 from Siphoviridae bacteriophage SPP1 is a tail completion protein located at the interface between the connector protein gp16 and the tail of bacteriophage SPP1 . Gp17 plays a fundamental role in the head-to-tail joining reaction, the ultimate step of virus particle assembly .
Protein of unknown function DUF3169 (DUF3169)
Type: Family

Some members in this family of proteins are annotated as membrane proteins however this cannot be confirmed. Currently there is no known function.
Protein of unknown function DUF3172 (DUF3172)
Type: Family

This family of proteins has no known function.
Protein of unknown function DUF3173 (DUF3173)
Type: Family

This family of proteins with unknown function appears to be restricted to Firmicutes.
Ralstonia phage RSL1, Orf186 (Phage_RSL1_Orf186)
Type: Family

This entry is represented by Ralstonia phage RSL1, Orf186. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.

This family of proteins with unknown function appears to be restricted to Proteobacteria.
Protein of unknown function DUF3176 (DUF3176)
Type: Family

This eukaryotic family of proteins has no known function.
Protein of unknown function DUF3177 (DUF3177)
Type: Family

Some members in this family of proteins are annotated as membrane proteins however this cannot be confirmed. Currently there is no known function.
Protein of unknown function DUF3179 (DUF3179)
Type: Family

This family of proteins has no known function.
Protein of unknown function DUF3180 (DUF3180)
Type: Family

Some members in this family of proteins are annotated as membrane proteins however this cannot be confirmed. Currently there is no known function.
Protein of unknown function DUF3181 (DUF3181)
Type: Family

This family of proteins has no known function.
Protein of unknown function DUF3182 (DUF3182)
Type: Family

This family of proteins with unknown function appears to be restricted to Proteobacteria.
Stealth protein CR2, conserved region 2 (Stealth_CR2)
Type: Domain

Stealth_CR2 is the second of several highly conserved regions on stealth proteins in metazoa and bacteria. There are up to four CR regions on all member proteins. CR2 carries a well-conserved NDD sequence-motif. The domain is found in tandem with CR1, CR3 and CR4 on both potential metazoan hosts and pathogenic eubacterial species that are capsular polysaccharide phosphotransferases. The CR domains appear on eukaryotic proteins such as GNPTAB, N-acetylglucosamine-1-phosphotransferase subunits alpha/beta. Horizontal gene-transfer seems to have occurred between host and bacteria of these sequence-regions in order for the bacteria to evade detection by the host innate immune system .
Protein of unknown function DUF3185 (DUF3185)
Type: Family

Some members in this bacterial family of proteins are annotated as membrane proteins however this cannot be confirmed. Currently no function is known.
Copper transporter MctB (MctB)
Type: Family

Outer membrane channel protein MctB in Mycobacterium tuberculosis is part of a Cu resistance mechanism that ensures low intracellular Cu levels in the bacterium. Human resistance to bacteria, mediated via IFN-gamma mediated activation of macrophages, may involve the use of reactive Cu(1) in the presence of hydrogen peroxide, since activated Cu is toxic to bacteria. IFN-gamma stimulates the trafficking of the Cu transporter ATP7a to the vesicles that fuse with phagosomes and these phagosomes are found to have a high Cu content and an increased bactericidal activity against E.coli. Using MctB, Mycobacterium tuberculosis may limit the amount of excess Cu within it whole in the host . MctB is involved copper resistance, but it is unclear whether it plays a direct role in copper efflux .
Protein of unknown function DUF3187 (DUF3187)
Type: Family

This family of proteins with unknown function appear to be restricted to bacteria.
Protein of unknown function DUF3188 (DUF3188)
Type: Family

This bacterial family of proteins has no known function.
Protein of unknown function DUF3189 (DUF3189)
Type: Family

This family of proteins with unknown function appears to be restricted to Firmicutes
Vitelline envelope, lysin receptor (Vitelline_env_lysin-recpt)
Type: Family

VERL (Vitelline envelope sperm lysin receptor) is a giant unbranched glycoprotein comprising 30% of the vitelline envelope. It functions as a species-specific receptor for the sperm protein lysin; prevents fertilisation by sperm from other species .
Protein of unknown function DUF2795 (DUF2795)
Type: Family

This family of proteins has no known function.
Phagosome trafficking protein DotA (DotA)
Type: Family

DotA is essential for intracellular growth in Legionella . DotA is thought to play an important role in regulating initial phagosome trafficking decisions either upon or immediately after macrophage uptake .
Protein of unknown function DUF2798 (DUF2798)
Type: Family

This family of proteins has no known function.
Oxamate carbamoyltransferase subunit AllH-like (AllH-like)
Type: Family

This entry, previously known as DUF2877, represents the Oxamate carbamoyltransferase subunit AllH and related bacterial proteins. AllH is a component of a carbamoyltransferase involved in the anaerobic nitrogen utilization via the assimilation of allantoin . It catalyses the conversion of oxalurate (N-carbamoyl-2-oxoglycine) to oxamate and carbamoyl phosphate.
Type VI lipase adapter protein Tla3, N-terminal domain (Tla3_N)
Type: Domain

This entry represents the N-terminal domain of Type VI lipase adapter protein Tla3, an adapter protein that targets and loads the Tle3 toxin onto the H2 type VI secretion system (H2-T6SS) machinery through an interaction with the TTR domain of VgrG2b and it seems specific for Tle3 . This domain and its C-terminal (

), are both required for the interaction with the toxin .
Structural accessory protein ORF7b, betacoronavirus (NS7B_bCoV)
Type: Family

This entry corresponds to ORF7b (also known as accessory protein 7b, NS7B, and 7b) from human SARS coronavirus (SARS-CoV) and SARS-CoV-2, which belong to the betacoronavirus B lineage (Sarbecovirus) .

ORF7b/NS7b from betacoronavirus in the B lineage are not related to NS7b proteins from other betacoronavirus lineages. The SARS-CoV ORF7b protein is a 44 amino acid protein which is homologous to an accessory but structural component of SARS-CoV virion. While ORF7b is packaged into virions, it is not required for the virus budding process, as gene 7 deletion viruses replicate efficiently in vitro and in vivo. Moreover, ORF7b possesses a transmembrane helical domain (TMD), between 9-29 amino acid residues, is necessary for its Golgi complex localization, as replacing it with the TMD from the human endoprotease furin results in aberrant localization .

ORF7b from SARS-CoV-2 is a 43 amino acid protein localized in the membrane of the endoplasmic reticulum and it has been shown to induce apoptosis. It promotes expression of IFN-beta, TNF-alpha, and IL-6, and activation of type-I IFN signaling through IRF3 phosphorylation and to activate TNFalpha-induced apoptosis in HEK293T cells and Vero E6 cells . These recent findings suggest a mechanism to understand pathogenicity of SARS-CoV-2 and the role of its accessory proteins in modulating host immune responses.
Putative beta-lactamase-inhibitor-like, PepSY-like (PepSY-like)
Type: Domain

This entry represents a domain found in a group of bacterial proteins that are probably periplasmic. Members are found predominantly in microbes of the human gut and oral cavity. Structurally, one member of this family is found to show similarity to the beta-lactamase-inhibitor PepSY proteins, so the overall function may be inhibitory. There are tandem repeats of the domain on many members .
Protein of unknown function DUF3192 (DUF3192)
Type: Family

Some members in this family of proteins are annotated as lipoproteins however this cannot be confirmed.
Tetrabrachion (Tetrabrachion)
Type: Family

Tetrabrachion forms a parallel right-handed coiled coil structure with hydrophobic interactions and salt bridges forming a thermostable tetrameric structure. It contains large hydrophobic cavities. No function is known for this family of proteins .
DNA ligase IV domain (DNA_ligase_IV_dom)
Type: Domain

This entry represents the DNA ligase IV (Lig4) sequences between the two BRCA1 C-terminal (BRCT) domains. Lig4 along with Xrcc4 functions in DNA non-homologous end joining. This process is required to mend double-strand breaks. Upon ligase binding to an Xrcc4 dimer, the helical tails unwind leading to a flat interaction surface .
Hypoxia-inducible factor, alpha subunit-like (HIF_alpha-like)
Type: Domain

Hypoxia-inducible factors (HIFs) are transcription factors that respond to changes in available oxygen in the cellular environment. Specifically, they respond to decreases in oxygen, mediating the effects of hypoxia . HIFs are heterodimers, composed of an alpha and a beta subunit. At least 3 different alpha subunits are known to exist, termed HIF-1, -2 and -3 alpha. Beta subunits, meanwhile, are constitutively-expressed aryl hydrocarbon receptor nuclear translocators (ARNTs).

In addition to their role in hypoxia, HIFs have been shown to be involved in a range of processes, including angiogenesis, metal transport, mitochondrial function and cell growth .

This entry represents a domain found in HIF alpha subunits and endothelial PAS domain-containing protein 1 (HIF1-alpha-like).
Syntaxin-5, N-terminal, Sly1p-binding domain (Syntaxin-5_N)
Type: Domain

This entry represents the Sed5 N-terminal and the N terminus of Syntaxin-5-like proteins. It is the region of Syntaxin that interacts with Sly1p, a positive regulator of intracellular membrane fusion, allowing SM (cytosolic Sec1/munc18-like) proteins to stay associated with the assembling fusion machinery. This allows the SM proteins to participate in late fusion steps .
Bacteriocin subtilosin A (Subtilosin_A)
Type: Family

This entry includes bacteriocins such as Subtilosin A and Mejucin from Bacillus subtilis. Subtilosin A has a cyclized peptide backbone and forms three cross-liks between the sulphurs of Cys13, Cys7 and Cys4 and the alpha-positions of Phe22,Thr28 and Phe31 .
PAE0736-like, N-terminal domain (PAE0736-like_N)
Type: Domain

This entry represents the N-terminal domain of the highly thermostable protein PAE0736 from Pyrobaculum aerophilum (

) and similar disulphide-rich uncharacterised proteins from thermophilic archaea. PAE0736, which shows three disulphide bonds, may play a role in the formation or maintenance of intracellular protein disulfide bonds in disulfide-rich organisms. This domain harbours two of these disulphide bonds. However, its specific function is still unknown .
Tn7 transposition regulator TnsC (Tn7_TnsC)
Type: Family

TnsC is a molecular switch that regulates transposition and interacts with TnsA which is a component of the transposase. The two proteins interact via the residues 504-555 on TnsC. The TnsA/TnsC interaction is very important in Tn7 transposition .
Programmed cell death activator EGL-1 (EGL-1)
Type: Family

Initiation of programmed cell death in C.elegans occurs by the binding of EGL-1 to CED-9 which disrupts a complex involving CED-4/CED-9 and allows CED-4 to activate CED-3, a caspase. It is the C-terminal domain of EGL-1 which is involved in the formation of the complex with CED-9. The formation of the complex induces structural rearrangements in CED-9 and EGL-1 adopts an extended α-helical conformation .
Vanadium-binding protein 2 (Vanabin-2)
Type: Family

The Vanadium binding protein, Vanabin2, contains four α-helices connected by nine disulphide bonds. Vanadium accumulates in Ascidians however the biological reason remains unclear .
Type III secretion system filament chaperone CesA (CesA)
Type: Family

This family represents a chaperone protein for the type III secretion system (TTSS) translocon protein EspA, to prevent the latter's self-polymerisation. The TTSS is a highly specialised bacterial protein secretory pathway, similar in many ways to the flagellar system, that is essential for the pathogenesis of many Gram-negative bacteria. The twenty or so proteins making up the TTSS apparatus, referred to as the needle complex, allow the injection of virulence proteins (known as effectors) directly into the cytoplasm of the eukaryotic host cells they infect; however, the injection process itself is mediated by a subset of extracellular proteins that are secreted by the needle complex to the bacterial surface and assembled into the type III translocon - EspA, EspB and EspD. EspA polymerises into an extracellular filament, and, as with other fibrous proteins, is apt to undergo massive polymerisation when overexpressed. CesA is the secretion chaperone protein that binds to EspA. CesA is dimeric and helical, and it traps EspA in a monomeric state and inhibits its polymerisation .
Pilot protein MxiM (MxiM)
Type: Family

MxiM, a Shigella pilot protein (also known as type 3 secretion system pilotin), is essential for the assembly and membrane association of the Shigella secretin MxiD. MxiM contains an orthologous secretin component and has a specific binding domain for the acyl chains of bacterial lipids . The C-terminal domain of MxiD hinders lipid binding to MxiM .
Protein of unknown function DUF2826 (DUF2826)
Type: Family

This is a family of uncharacterised proteins that is highly conserved in Trypanosoma cruzi.
Protein of unknown function DUF2895 (DUF2895)
Type: Family

This is a bacterial family of uncharacterised proteins. Members of this entry are found occasionally on plasmids such as the Pseudomonas putida TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition.
Protein of unknown function DUF2894 (DUF2894)
Type: Family

This is a bacterial family of uncharacterised proteins.
Protein of unknown function DUF2897 (DUF2897)
Type: Family

This is a bacterial family of uncharacterised proteins.
Protein of unknown function DUF3005 (DUF3005)
Type: Family

This is a bacterial family of uncharacterised proteins.
Putative, 10TM heavy-metal exporter (ArsP_2)
Type: Family

This is a family of putative heavy metal transporters with 8-11 TMs. Members carry two well-conserved characteristic sequence- motifs of 'PGCG'. It has been reported that some proteins of this family are involved in arsenate/arsenite resistance. Other members are annotated as manganese transporters.
Protein of unknwon function DUF3008 (DUF3008)
Type: Family

This is a bacterial family of uncharacterised proteins.
Protein of unknown function DUF3000 (DUF3000)
Type: Family

This is a bacterial family of uncharacterised proteins.
Protein of unknown function DUF2950 (DUF2950)
Type: Family

This is a bacterial family of uncharacterised proteins.
Protein of unknown function DUF3016 (DUF3016)
Type: Family

This is a bacterial family of uncharacterised proteins.
Antitoxin MazE-like (MazE-like)
Type: Family

This entry includes MazE from Mycobacterium smegmatis. MazE is an antitoxin component of a type II toxin-antitoxin (TA) system .
Protein of unknown function DUF3019 (DUF3019)
Type: Family

This is a bacterial family of uncharacterised proteins.
Protein of unknown function DUF3021 (DUF3021)
Type: Family

This is a bacterial family of uncharacterised proteins.
Transcriptional regulator, AbiEi 3 antitoxin, Type IV TA system (AbiEi_3)
Type: Family

AbiEi 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 .
Protein of unknown function DUF3007 (DUF3007)
Type: Family

This is a family of uncharacterised proteins found in bacteria and eukaryotes.
Rab interacting lysosomal protein, dimerization domain (RILP_dimer)
Type: Domain

Rab interacting lysosomal protein (RILP) contains a domain which contains two coiled-coil regions and is found mainly in the cytosol. RILP is recruited onto late endosomal and lysosomal membranes by Rab7 and acts as a downstream effector of Rab7 . This recruitment process is important for phagosome maturation and fusion with late endosomes and lysosomes.
Protein of unknown function DUF3203 (DUF3203)
Type: Family

This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.
Rabenosyn, Rab binding domain (Rbsn_Rab-bd)
Type: Domain

Rabenosyn-5 (Rbsn) is a multivalent effector with interacts with the Rab family. Rsbn contains distinct Rab4 and Rab5 binding sites within residues 264-500 and 627-784 respectively . Rab proteins are GTPases involved in the regulation of all stages of membrane trafficking .
Prion-like protein Doppel (Doppel)
Type: Family

Dpl is a homologue related to the prion protein (PrP). Dpl is toxic to neurons and is expressed in the brains of mice that do not express PrP. In DHPC and SDS micelles, Dpl shoes about 40% α-helical structure however in aqueous solution it consists of a random coil. The α helical segment can adopt a transmembrane localisation also in a membrane. The unprocessed Dpl protein is thought to posses a possible channel formation mechanism which may be related to toxicity through direct interaction with cell membranes and damage to the cell membrane.