SII-SWORD/CoKE huggingface dataset:
Protein of unknown function DUF5320 (DUF5320)
Type: Family

This is a family of unknown function mainly found in bacteria and archaea. A number of this family members have a coiled coil domain at their C terminus.
Proteasome subunit beta 2 (Proteasome_beta2)
Type: Family

This entry includes the constitutive proteasome subunit beta 2 (MEROPS identifier T01.984), also known as HC7 , Prosbeta4 (in
Drosophila melanogaster
), and PRE1 or beta 4 (in
Saccharomyces cerevisiae
) . This entry also includes Prosbeta4R1 and Prosbeta4R2 subunits from the
D. melanogaster
spermatoproteasome .
Protein of unknown function DUF5457 (DUF5457)
Type: Family

This is a family of unknown function found in bacteria. Family members have one predicted trans-membrane region.
Floricaula/leafy, DNA-binding C-terminal domain (FLO/LFY_C)
Type: Domain

This domain is found in various plant development proteins which are homologues of floricaula (FLO) and Leafy (LFY) proteins which are floral meristem identity proteins. Mutations in the sequences of these proteins affect flower and leaf development. LFY is a plant-specific transcription factor (TF) essential for flower development. It is one of the few master regulators of flower development, as it integrates environmental and endogenous signals to orchestrate the whole floral network. Transcription factors such as LFY recognize short DNA motifs primarily through their DNA-binding domain. Upon binding to short stretches of DNA called cis-elements or TF binding sites (TFBS), they regulate gene expression.

This entry represents the DNA binding domain found in C-terminal of LFY proteins in plants. Structure-function studies have demonstrated that LFY binds semi-palindromic 19-bp DNA elements through its highly conserved C-terminal DBD, a unique helix-turn-helix fold that by itself dimerizes on DNA .
Protein of unknown function DUF5455 (DUF5455)
Type: Family

This is a family of unknown function found in Proteobacteria. Family members contain three predicted trans-membrane regions.
Protein of unknown function DUF5325 (DUF5325)
Type: Family

This is a family of unknown function mainly found in Bacilli. Family members of this family are predicted to have trans-membrane domains.
Matrix/matrix long, N-terminal (Mx/ML_C)
Type: Domain

This entry represents the N-terminal domain of family members such as the Matrix (Mx) and Matrix protein long (ML) proteins. They are found in Thogoto virus (THOV), a tick-transmitted orthomyxovirus with a genome consisting of six single-stranded RNA segments that encode seven structural proteins . Matrix proteins of the family Orthomyxoviridae are major structural components of the viral capsid, located below the viral lipid membrane and provide protection for viral ribonucleoproteins (vRNPs) . They serve as a major participant during the processes of virus invasion and budding. Furthermore, they play specific roles throughout the viral life cycle, usually by interacting with other viral components or host cellular proteins .

ML protein, an extended version of the viral M protein, is a viral IFN antagonist. ML is essential for virus growth and pathogenesis in an IFN-competent host. In the presence of ML the activation and/or action of the interferon regulatory factor-3 (IRF-3) is severely affected. This effect depends on direct interaction of ML with the transcription factor IIB (TFIIB). ML suppresses IRF-7 in a similar manner as it suppresses IRF-3. Studies have revealed that ML associates with IRF-7 and prevents IRF-7 dimerization and interaction with TRAF6 .

Structural analysis revealed that N-terminal fragment of M protein (MN) undergoes conformational changes that result in specific, pH-dependent inter-molecular interactions. Comparison of THOV MN and influenza A virus (IAV) MN region, showed low sequence identity. However, superimposition of the two structures in neutral condition showed that both matrix proteins contain nine helices connected with same topology. Since the matrix layer of IAV disassembles in acidic endosome at the beginning of infection and repacks in the neutral cytoplasm, a change of pH might be a key regulator for the capsid assembly/disassembly transition during these processes. Hence, pH-dependent conformational transition model was studied in THOV MN, where interactions such as hydrogen bonds and hydrophobic interactions are suggested to be involved in THOV matrix assembly .
Protein of unknown function DUF5321 (DUF5321)
Type: Family

This is a family of unknown function. Most of the members seem to carry one trans-membrane region.
Protein of unknown function DUF5324 (DUF5324)
Type: Family

This is a family of unknown function, mostly found in Actinobacteria. Most of the family members contain one trans-membrane domain.
Protein of of unknown function DUF5454 (DUF5454)
Type: Family

This is a family of unknown function found in Mycoplasma.
Protein of unknown function DUF5453 (DUF5453)
Type: Family

This is a family of unknown function found in Mycoplasma. Family members have 4 predicted trans-membrane regions.
Protein of unknown function DUF5327 (DUF5327)
Type: Family

This bacterial family of proteins has no known function and is mostly found in Bacilli.
Protein of unknown function DUF5452 (DUF5452)
Type: Family

This is a family of unknown function found in Mycoplasmataceae.
Protein of unknown function DUF5330 (DUF5330)
Type: Family

This is a family of unknown function mostly found in Bacteria.
Protein of unknown function DUF5451 (DUF5451)
Type: Family

This is a family of unknown function found in Epstein-Barr virus.
Non-structural protein NS3 (NS3)
Type: Family

This is a family of proteins found in viruses. Members of this family such as NS3 found in Junonia coenia have been shown to be involved in viral DNA replication. Generation of deletion mutants and replicative cycle analysis show that NS3 is required for viral DNA replication . Bioinformatics analysis of Bombyx mori densovirus protein NS3, show that it has two putative zinc-finger motifs, 6 putative N glycosylation sites, and 4 putative phosphorylation sites .
Protein of unknown function DUF5335 (DUF5335)
Type: Family

This bacterial family of proteins has no known function.
TcfC, Usher-like barrel domain (Usher_TcfC)
Type: Domain

This is the presumed β barrel domain from the usher-like TcfC family of proteins.
Protein of unknown function DUF5338 (DUF5338)
Type: Family

This is a family of unknown function which can be found mostly in Proteobacteria. Proteins in this entry include protein TraK from Escherichia coli.
Protein of unknown function DUF5450 (DUF5450)
Type: Family

This is a family of unknown function found in Giardia intestinalis.
Protein HdcB (HdcB)
Type: Family

This family represents histidine decarboxylase maturation protein HdcB, mainly found in Lactobacillus. HdcB performs a cleavage and modification of the pyruvoyl-dependent histidine decarboxylase HdcA, generating the pyruvoyl prosthetic group .
Protein of unknown function DUF5340 (DUF5340)
Type: Family

This family of unknown function can be found in Cyanobacteria.
Lysogeny maintenance PflM (PflM)
Type: Family

This is a family of proteins related to lysogeny maintenance protein PflM. These proteins contain several conserved cysteine and histidine residues that may form zinc binding sites .
Anti-sigma factor CnrY (CnrY)
Type: Family

This family is found in alpha and beta proteobacteria. Family members include anti-sigma factor CnrY from Cupriavidus metallidurans.

Sigma factors are multi-domain subunits of bacterial RNA polymerase (RNAP) that play critical roles in transcription initiation, including the recognition and opening of promoters as well as the initial steps in RNA synthesis. They also control a wide variety of adaptive responses such as morphological development and the management of stress. A recurring theme in sigma factor control is their sequestration by anti-sigma factors that occlude their RNAP-binding determinants . CnrH controls cobalt and nickel resistance in Cupriavidus metallidurans. CnrH is regulated by a complex of two transmembrane proteins: the periplasmic sensor CnrX and the anti-sigma CnrY. At rest, CnrH is sequestered by CnrY whose 45-residue-long cytosolic domain is one of the shortest anti-sigma domains. Upon Ni(II) or Co(II) ions detection by CnrX in the periplasm, CnrH is released between CnrH and the cytosolic domain of CnrY (CnrYc). The CnrH/CnrYC complex displays an unexpected structural similarity to the anti-sigma NepR in complex with its antagonist PhyR, whereas NepR shares no sequence similarity with CnrY. Crystal structure of CnrH/CnrY shows that CnrYC residues 3-19 are folded as a well-defined α-helix. The peptide further extends along the hydrophobic groove of sigma 2 with no canonical structure except for a short helical turn spanning residues 24-28. CnrY has a hydrophobic knob made of V4, W7 and L8 side chains protruding into sigma 4 hydrophobic pocket and contributing to the interface. In vivo investigation of CnrY function pinpoints part of the hydrophobic knob as a hotspot in CnrH inhibitory binding .
Protein of unknown function DUF5346 (DUF5346)
Type: Family

This family of unknown function is found in Nematoda.
Protein of unknown function DUF5347 (DUF5347)
Type: Family

This family of unknown function is found mainly in Proteobacteria.
Protein of unknown function DUF5443 (DUF5443)
Type: Family

This is a family of unknown function found in Mycoplasma.
IgGFc-binding protein, N-terminal (IgGFc-bd_N)
Type: Domain

This domain is found at the N terminus of

and has been shown to confer IgG Fc binding activity . It may play a role in immune protection and inflammation in the intestines of primates .
Protein of unknown function DUF5343 (DUF5343)
Type: Family

This is a family of unknown function mostly found in Bacteria.
RNA chaperone ProQ, C-terminal (ProQ_C)
Type: Domain

This domain is found at the C terminus of many ProQ proteins.

ProQ is a RNA chaperone with significant RNA binding, RNA strand exchange and RNA duplexing activities. It may regulate ProP activity through an RNA-based, post-transcriptional mechanism. It contains a FinO-like domain that serves as a high-affinity RNA-binding domain and a Hfq-like domain that is largely responsible for RNA strand exchange and duplexing .
Protein of unknown function DUF5341 (DUF5341)
Type: Family

This is a family of unknown function, which can be found mostly in Ascomycota.
Protein of unknown function DUF5345 (DUF5345)
Type: Family

This is a family of unknown function. It is found mostly in Bacteria. Members of this family are predicted to contain two trans-membrane regions.
Cypovirus polyhedrin (CPV_Polyhedrin)
Type: Family

This family is found in polyhedrin proteins of Cypoviruses. These viruses possess a single capsid layer with turrets and are commonly embedded in crystalline occlusion bodies called polyhedra, which are formed in the cell cytoplasm and mainly composed of a single virus-encoded protein, polyhedron. Cypoviruses have been classified into 21 distinct types. Within each type the amino acid sequence of polyhedrins are highly conserved, whilst between types there is little conservation. Structural analysis and comparison of the different polyhedrins reveals five variable regions: the N-terminal loop, connections between secondary structures (H2 and H3, beta-E and beta-F, beta-F and beta-G, beta-G and beta-H), and the C-terminal loop, which is designate V1-V5 respectively. V2 forms a 'cap' at one end of the protein and is subdivided across two sections of the polypeptide, V2n and V2c. Differences in these regions give each polyhedrin its characteristic appearance. The base domain (residues 74-110) is a region that is neither required for proper folding of the protein, nor for crystal assembly, but fine-tunes the crystal, 'locking-down' the structure, often in conjunction with NTPs. This region is also implicated in virion recognition and packaging .
SprT-like, zinc ribbon domain (SprT_Zn_ribbon)
Type: Domain

This entry represents a domain found in eukaryotes and prokaryotes. The domain contains a characteristic motif of the zinc ribbon. Proteins containing this domain includes the bacterial SprT protein.
Domain of unknown function DUF5442 (DUF5442)
Type: Domain

This domain is found in a group of proteins from non-biting midges (Chironomidae), including Balbiani ring A 67 kDa protein from Chironomus thummi thummi. These proteins are encoded by genes contained in Balbiani ring A, a large puff (active region) on the polytene chromosomes of Chironomus .
Protein of unknown function DUF5329 (DUF5329)
Type: Family

This is a bacterial family of proteins with unknown function, mostly found in Proteobacteria.
TamA, POTRA domain 1 (TamA_POTRA_Dom_1)
Type: Domain

This family represents the first POTRA domain found in the membrane insertase TamA, which is involved in autotransporter biogenesis .

In Gram-negative bacteria, β-barrel proteins are integrated into the outer membrane by the β-barrel assembly machinery, with key components of the machinery being the Omp85 family members BamA and TamA . The BamA periplasmic domain is composed of five globular subdomains in tandem called POTRA motifs. They are key to BAM complex formation and interaction with the substrate β-barrel proteins . TamA has three periplasmic POTRA domains . Outer mebrane proteins with a variable number of POTRA motifs are also found in mitochondria and chloroplasts .
Spermidine synthase, tetramerisation domain (Spermidine_synt_N)
Type: Domain

This entry represents the N-terminal tetramerization domain of spermidine synthase . Spermidine synthase is involved in the first step of the spermidine biosynthesis subpathway that synthesizes spermidine from putrescine.
PRMT5, TIM barrel domain (PRMT5_TIM)
Type: Domain

This entry represents the N-terminal TIM barrel domain of PRMT5.

Proteins containing this domain includes Skb1 from S. pombe , Hsl7 from S. cerevisiae and their homologues PRMT5 from animals and plants . Skb1 is a mediator of hyperosmotic stress response in Schizosaccharomyces pombe . Plant PMRT15 is involved in the post-transcriptional regulation of the circadian clock . Human PRMT5 is a component of multiple protein complexes and contributes to essential cellular processes, such as RNA transport and splicing, cell cycle regulation, tumour growth, and chromatin remodelling, leading to either gene silencing or activation .
PRMT5, oligomerisation domain (PRMT5_C)
Type: Domain

This entry represents the C-terminal oligomerisation domain of PRMT5.

Proteins containing this domain includes Skb1 from S. pombe , Hsl7 from S. cerevisiae and their homologues PRMT5 from animals and plants . Skb1 is a mediator of hyperosmotic stress response in Schizosaccharomyces pombe . Plant PMRT15 is involved in the post-transcriptional regulation of the circadian clock . Human PRMT5 is a component of multiple protein complexes and contributes to essential cellular processes, such as RNA transport and splicing, cell cycle regulation, tumour growth, and chromatin remodelling, leading to either gene silencing or activation .
Protein of unknown function DUF5441 (DUF5441)
Type: Family

This is a family of unknown function found in Mastadenoviruses.
Metapneumovirus small hydrophobic protein (Metap_SH)
Type: Family

This family is found in SH (small hydrophobic) proteins present in Metapneumovirus such as the Avian metapneumovirus (AMPV), a paramyxovirus that has three membrane proteins (G, F, and SH). Among them, the SH protein is a small type II integral membrane protein. It is located in both the plasma membrane as well as within intracellular compartments. AMPV type C- SH protein localizes in the endoplasmic reticulum (ER), Golgi, and cell surface, and is transported through ER-Golgi secretory pathway. AMPV SH protein is modified by N-linked glycans and can be released into the extracellular environment. Furthermore, it has been shown that glycosylated AMPV SH proteins form homodimers through cysteine-mediated disulfide bonds .
ShlB, POTRA domain (ShlB_POTRA)
Type: Domain

This entry represents the second POTRA domain (for polypeptide-transport-associated domain) found in the ShlB family proteins. ShlB is important in the secretion and activation of the haemolysin ShlA .
Gene product 44 (Gp44)
Type: Family

This is a family with unknown function.
Putative lipoprotein, bacteria (Lipoprotein_22_bac)
Type: Family

All the proteins in this family have a N-terminal lipoprotein attachment motif. No member of this family has been functionally characterised. Proteins in this family are found in Firmicute bacteria.
Domain of unknown function DUF5348 (DUF5348)
Type: Domain

This entry represents an uncharacterised domain found mostly in proteins from Firmicutes.
Protein of unknown function DUF5349 (DUF5349)
Type: Family

This is a family of unknown function found in Saccharomycetaceae.
Protein of unknown function DUF5350 (DUF5350)
Type: Family

This family is found in Euryarchaeota, predominantly in Methanomicrobia and Archaeoglobi. No known function for this family has been demonstrated.
Protein of unknown function DUF5437 (DUF5437)
Type: Family

This is a family of unknown function found in Alphabaculovirus.
Filaments in between nuclei protein-1 (Fin1)
Type: Family

Fin1 forms filaments between the spindle pole bodies of dividing cells and localizes to spindle microtubules during anaphase. It contributes to spindle stability. The C-terminal half of Fin1 contains coiled-coil motifs that are required for its self-association. The N-terminal half of Fin1 can be phosphorylated at multiple sites by the cyclin-dependent kinase Clb5-Cdk1, and dephosphorylation in anaphase triggers its localization to the spindle .
Protein of unknown function DUF5435 (DUF5435)
Type: Family

This is a family of unknown function found in Varicellovirus.
Protein of unknown function DUF5434 (DUF5434)
Type: Family

This is a family of unknown function found in Varicellovirus.
Colicin-K immunity (Colicin-K_immunity)
Type: Family

Colicins are bacterial toxins produced by Escherichia coli strains and are active against E. coli or related strains. These bacterial antibiotic toxins play an important role in the E. coli colonization of environmental niches. Colicin K uses the Tsx nucleoside-specific receptor for binding at the cell surface, the OmpA protein for translocation through the outer membrane, and the TolABQR proteins for the transit through the periplasm. The N-terminal domain interacts with components of its import machinery, including the TolB and TolQ proteins . Members of this family are colicin K immunity proteins. These proteins are able to protect a cell against colicin K .
26S Proteasome non-ATPase regulatory subunit 9 (PSMD9)
Type: Family

This entry represents non-ATPase regulatory subunit 9 of the 26S proteasome (gene name PSMD9), also known as p27, which is not a component of the assembled 26S proteasome, but is a chaperone required for assembly forming part of the base assembly and of the modulator trimer complex of PSMD9 (p27), PSMC6 (Rpt4) and PSMC3 (Rpt5) .
Protein of unknown function DUF5433 (DUF5433)
Type: Family

This is a family of unknown function found in Orthopoxviruses.
Protein of unknown function DUF5432 (DUF5432)
Type: Family

This is a family of unknown function found in Orthopoxvirus.
Protein of unknown function DUF5351 (DUF5351)
Type: Family

This family of unknown function is found in Bacillales.
Protein of unknown function DUF5431 (DUF5431)
Type: Family

This is a family of unknown function found in Enterobacteriaceae.
Protein of unknown function DUF5352 (DUF5352)
Type: Family

This is a family of unknown function found mostly in Nematoda.
Small integral membrane protein 3 (Smim3)
Type: Family

Smim3 (Small integral membrane protein 3) also known as NID67 (NGF-induced differentiation clone 67) may be involved in forming or regulating ion channels in neuronal differentiation. It is strongly induced by NGF (Nerve Growth Factor) and FGF (Fibroblast Growth Factor), both of which cause these cells to differentiate. The amino acid sequence of NID67 is strongly conserved among rat, mouse and human. This family of small membrane proteins is only 60 amino acids long and analysis of the predicted peptide sequence reveals a stretch of 29 hydrophobic and uncharged residues which very likely comprise a trans-membrane region . SMIM3 has been found highly expressed in adult AML, which was associated with a poor prognosis in adult AML. Knockdown of SMIM3 inhibited the proliferation of AML through regulation of the PI3K-AKT signalling pathway, making SMIM3 a potential prognostic marker and a therapeutic target for AML .
Feline immunodeficiency virus OrfA protein (FIV_OrfA)
Type: Family

OrfA protein is a multifunctional accessory protein found in Feline immunodeficiency virus (FIV), a lentivirus that causes AIDS in domestic cats . Multiple potential functions have been ascribed to OrfA, including transactivation of viral protein expression , effects on virion formation and infectivity , host cell cycle arrest and downregulation of cell surface expression of the primary FIV receptor, CD134 .
MalF, N-terminal (MalF_N)
Type: Homologous_superfamily

The malF gene product (MalF) is an inner membrane component of the maltose transport system in Escherichia coli. Some gene fusions between malF and lacZ produce hybrid proteins which are membrane-bound while other fusions produce hybrid proteins which are cytoplasmic .

The MalF protein belongs to the ABC transporter superfamily, the binding-protein-dependent transport system permease family and the MalFG subfamily. Hydrophobic proteins from the ABC transporter superfamily display a conserved, at least 20 amino acid region (EAA-X3-G-X9-I-X-LP), exposed in the cytosol, called the EAA region. This region is presume to be a recognition site for the ABC ATPase helical domain .
Protein of unknown function DUF5355 (DUF5355)
Type: Family

This family of unknown function is found in Saccharomycetales.
Protein of unknown function DUF5358 (DUF5358)
Type: Family

This family of unknown function is found in Proteobacteria.
Bacteriocin helveticin-J (Helveticin_J)
Type: Family

Bacteriocins are biologically active proteins or protein complexes that display a bactericidal mode of action towards closely related species . Bacteriocins produced by lactic acid bacteria are grouped into different classes. Class III of bacteriocins includes large heat liable proteins . Lactobacillus helveticus 481 produces a 37kDa bacteriocin called helveticin J which is a representative for Clas III bacteriocins .
Protein of unknown function DUF5359 (DUF5359)
Type: Family

This is a family of unknown function found in Bacillales. Most of the family members are predicted to have one trans-membrane region.
Protein of unknown function DUF5429 (DUF5429)
Type: Family

This is a family of unknown function found in Human cytomegalovirus.
Protein Fmp23 (Fmp23)
Type: Family

FMP23 gene encodes a putative mitochondrial protein involved in iron-copper homoeostasis. It was observed to be induced in response to ATX1 deletion and high copper conditions .
Protein of unknown function DUF5428 (DUF5428)
Type: Family

This is a family of unknown function found in Betanecrovirus.
Ctenitoxin (CNTX)
Type: Family

This family includes peptides isolated from Phoneutria such as delta-ctenitoxins. Members of the CNTX-Pn1a family and its paralogues (delta-CNTX-Pn1b through delta-CNTX-Pn1e) of Phoneutria toxins have complex effects on sodium channels, but their primary effect appears to be an inhibition of channel inactivation, a pharmacology similar to that of the delta-atracotoxins and delta-conotoxins. Orthologous toxins such as delta-CNTX-Pr1/PK1 and Pn2 are also family members, some of which act by blocking the calcium channels . Delta-CNTX-Pn1a and delta-CNTX-PN2a are 48-amino-acid polypeptides, with 5 disulfide bridges . The later has a complex pharmacology that results in inhibition of NaV channel inactivation and a hyperpolarizing shift in the channel activation potential .
Protein of unknown function DUF5361 (DUF5361)
Type: Family

This is a family of unknown function found in bacteria and virus.
Protein of unknown function DUF5362 (DUF5362)
Type: Family

This is a family of unknown function found in Bacteria. Most of the family members are predicted to have 2 trans-membrane regions.