SII-SWORD/CoKE huggingface dataset:
Protein of unknown function DUF3755 (DUF3755)
Type: Family

This domain family is found in eukaryotes, and is approximately 40 amino acids in length. There is a single completely conserved residue N that may be functionally important.
Tripeptidyl peptidase II, second Ig-like domain (TPPII_Ig-like-2)
Type: Domain

This entry represents the second Ig-like domain found in the central region of tripeptidyl peptidase II (TPPII, MEROPS peptidase family S8A). TPPII is a crucial component of the proteolytic cascade acting downstream of the 26S proteasome in the ubiquitin-proteasome pathway. It is an amino peptidase belonging to the subtilase family removing tripeptides from the free N terminus of oligopeptides . It consists of three main parts: the N-terminal subtilisin-like domain (

), a central domain and a C-terminal domain . According to the structures, the central domain can be subdivided into Ig-like and galactose-binding domain-like (GBD).
Protein of unknown function DUF3756 (DUF3756)
Type: Family

This domain family is found in viruses, and is approximately 40 amino acids in length.
Protein of unknown function DUF3757 (DUF3757)
Type: Family

This family of proteins is found in bacteria. Proteins in this family are typically between 94 and 154 amino acids in length.
Tripeptidyl peptidase II, C-terminal domain, arthropoda (TPPII_C_art)
Type: Domain

This entry represents the C-terminal domain of tripeptidyl peptidase II (TPPII, MEROPS peptidase family S8A). TPPII is a crucial component of the proteolytic cascade acting downstream of the 26S proteasome in the ubiquitin-proteasome pathway. It is an amino peptidase belonging to the subtilase family removing tripeptides from the free N terminus of oligopeptides . It consists of three main parts: the N-terminal subtilisin-like domain (

), a central domain (

) and a C-terminal domain .
TRAPP II complex TRAPPC10, C-terminal (TRAPP_II_complex_TRAPPC10_C)
Type: Domain

The trafficking protein particle complex TRAPP is a multi-protein complex needed in the early stages of the secretory pathway. To date, two kinds of TRAPP complexes have been studied, TRAPPI and TRAPP II. These complexes differ in subunit composition . TRAPP I binds vesicles derived from the endoplasmic reticulum bringing them closer to the acceptor membrane.
Protein of unknown function DUF3759 (DUF3759)
Type: Family

This family of proteins is found in eukaryotes. Proteins in this family are typically between 107 and 132 amino acids in length. There is a single completely conserved residue H that may be functionally important.
Protein of unknown function DUF3760 (DUF3760)
Type: Family

This family is found in fungi, and is typically between 46 and 64 amino acids in length.
Protein of unknown function DUF3761 (DUF3761)
Type: Family

This family of proteins is found in bacteria. Proteins in this family are typically between 100 and 157 amino acids in length.
L-tryptophan decarboxylase PsiD-like (PsiD-like)
Type: Domain

This domain is found in bacteria and eukaryotes, and is approximately 140 amino acids in length. This domain is associated with the phosphatidylserine decarboxylase domain. Proteins containing this domain include PsiD from Psilocybe cubensis. PsiD is a L-tryptophan decarboxylase involved in psilocybin biosynthesis .
18S rRNA (guanine(1575)-N(7))-methyltransferase Bud23, C-terminal (Bud23_C)
Type: Domain

This entry represents the C-terminal domain of 18S rRNA (guanine(1575)-N(7))-methyltransferase Bud23 . Bud23 homologues can be found from yeast to human. They are S-adenosyl-L-methionine-dependent methyltransferases that specifically methylates the N7 position of a guanine in 18S rRNA . Bud23 homologue in Arabidopsis, known as Rid2 (ROOT INITIATION DEFECTIVE 2), is also involved in pre-rRNA processing .
Protein of unknown function DUF3762 (DUF3762)
Type: Family

This domain family is found in viruses, and is approximately 80 amino acids in length. The family is found in association with

.
Protein of unknown function DUF3764 (DUF3764)
Type: Family

This family of proteins is found in bacteria. Proteins in this family are typically between 89 and 101 amino acids in length.
Inactive rhomboid protein 1/2, N-terminal (iRhom1_2_N)
Type: Domain

This entry represents an N-terminal helical segment of inactive rhomboid proteins (iRhom1/2), which are catalytically inactive rhomboid protease homologues that play crucial roles within the secretory pathway, including protein degradation, trafficking regulation, and inflammatory signalling . These are metazoan specific pseudoproteases which regulate ADAM17 protease, a sheddase of the epidermal growth factor (EGF) receptor ligands and TNF, acting as trafficking factors that escort ADAM17 from the ER to the later secretory pathway. They are required for the cleavage and release of a variety of membrane-associated proteins . iRhoms share a common structure comprising 7-helix transmembrane-spanning domains (TMDs) which is a conserved rhomboid fold (

), an extended N-terminal cytosolic domain and a luminal loop .

These proteins have been linked to the development and progression of several autoimmune diseases including rheumatoid arthritis, lupus nephritis, as well as hemophilic arthropathy and also in neurological disorders such as Alzheimer's and Parkinson's diseases, inflammation, cancer and skin diseases .
Transposable element P transposase-like, C-terminal (TNP-like_C)
Type: Domain

This domain is found in arthropods, and is typically between 78 and 110 amino acids in length. It represents the C-terminal domain of transposable element P transposase (TNP) from Drosophila . TNP specifically mediates transposition of P-elements, being involved in both precise and imprecise excision. It has unique features such as the requirement for a guanosine triphosphate cofactor and the generation of long staggered DNA breaks during transposition. TNP structure revealed that it consists of several domains: THAP at the N-terminal, followed by a dimerization domain, a HTH domain, the catalytic RNase H domain is interrupted by a GTP-binding insertion domain (GBD) and a C-terminal one . The HTH, GBD and C-terminal domains are involved in protein-DNA interactions.
Protein of unknown function DUF3768 (DUF3768)
Type: Family

This family of proteins is found in bacteria. Proteins in this family are typically between 108 and 129 amino acids in length. There are two conserved sequence motifs: NDP and RVLT.
Protein of unknown function DUF3769 (DUF3769)
Type: Family

This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 560 and 931 amino acids in length.
Rubivirus non-structural protein, C-terminal (Rubi_NSP_C)
Type: Domain

This domain is found in viruses, and is approximately 70 amino acids in length. The family is found in association with

. The Rubella virus (RUB) nonstructural (NS) protein (NSP) ORF encodes a protease that cleaves the NSP precursor (240kDa) at a single site to produce two products.
Bacteriophage T7, Gp17, C-terminal (Phage_T7_Gp17_C)
Type: Domain

This domain is found in bacterial prophage and viruses, and is typically between 49 and 166 amino acids in length. The family is found in association with

. In T-even phages, Gp37 and Gp38 are components of the tail fibre that are critical for phage-host interaction .
Casein kinase 1 gamma C-terminal (Casein_kinase-1_gamma_C)
Type: Domain

This domain family is found in eukaryotes, and is typically between 54 and 99 amino acids in length. The family is found in association with

. CK1gamma is a membrane-bound member of the CK1 family. Gain-of-function and loss-of-function experiments show that CK1gamma is both necessary and sufficient to transduce LRP6 signalling in vertebrates and Drosophila cells.
TNF receptor family, RELT (TNF_rcpt_RELT)
Type: Family

The members of tumor necrosis factor receptor (TNFR) superfamily have been designated as the "guardians of the immune system" due to their roles in immune cell proliferation, differentiation, activation, and death (apoptosis).

RELT (receptor expressed in lymphoid tissues) is a member of the TNFR superfamily. The messenger RNA of RELT is especially abundant in hematologic tissues such as spleen, lymph node, and peripheral blood leukocytes as well as in leukemias and lymphomas. RELT is able to activate the NF-kappaB pathway and selectively binds tumor necrosis factor receptor-associated factor 1 . RELT like proteins 1 and 2 (RELL1 and RELL2) are two RELT homologues that bind to RELT. The expression of RELL1 at the mRNA level is ubiquitous, whereas expression of RELL2 mRNA is more restricted to particular tissues .
Domain of unknown function DUF3772 (DUF3772)
Type: Domain

This domain is found in bacteria, and is approximately 60 amino acids in length. The domain is found in association with

.
Type IVb secretion, IcmS, effector-recruitment (T4bSS_IcmS)
Type: Family

This entry represents a family of Gram-negative bacterial proteins involved in the Dot/Icm type IVb transport system, including IcmS from Legionella pneumophila. Members are small acidic cytoplasmic proteins required for Dot/Icm-dependent activities . IcmS is part of a subcomplex which recruits effector proteins and delivers them to the core transmembrane subcomplex .
Protein of unknown function wound-induced (DUF3774_wound-induced)
Type: Family

This family of proteins is found in eukaryotes. Proteins in this family are typically between 81 and 97 amino acids in length. The proteins in the family are often annotated as wound-induced proteins however there is little accompanying literature to confirm this.
SOCS4/SOCS5 domain (SOCS4/SOCS5_dom)
Type: Domain

Suppressors of cytokine signaling (SOCS) proteins play important roles in regulating a variety of signal transduction pathways that are involved in immunity, growth and development of organisms. They share a similar domain organisation, with a central SH2 domain and a conserved C-terminal SOCS box. In contrast, the N-terminal domains vary in length and amino acid sequence. In the case of SOCS4-7, the N-terminal domain accounts for a large proportion of the protein .

This entry represents a conserved region in the N-terminal domains of SOCS4 and 5. This domain is approximately 60 amino acids in length. It is found in association with

,

.
Ribosome recycling factor. bacterial (Ribosome_recyc_fac_bac)
Type: Family

This family of proteins is found in bacteria and viruses. Proteins in this family are approximately 130 amino acids in length. There are two conserved sequence motifs: LPS and LKR. Overproduction of ribosome recycling factor (RRF) reduces tna operon expression and increases the rate of cleavage of TnaC-tRNA(2)(Pro), relieving the growth inhibition associated with plasmid-mediated tnaC overexpression.
Protein of unknown function DUF3775 (DUF3775)
Type: Family

This family is found in bacteria. Proteins in this family have a single completely conserved residue G that may be functionally important.
PHD finger protein 20, AT hook (PHF20_AT-hook)
Type: Domain

PHD finger protein 20 (PHF20) is a Methyllysine-binding protein, component of the MOF histone acetyltransferase protein complex. It consists of tandem Tudor domains at the N-terminal, an AT hook, a C2H2-type zinc finger, and a plant homeodomain (PHD) finger . PHF20L1 binds to monomethylated lysine 142 on DNA (cytosine-5) methyltransferase 1 (DNMT1). It has been shown to antagonize DNMT1 proteasomal degradation .

This is the AT-hook domain found in PHD finger protein 20 (PHF20) and similar sequences from vertebrates .
Domain of unknown function DUF3778 (DUF3778)
Type: Domain

This domain is found in uncharacterised plant proteins, and is typically between 48 and 61 amino acids in length. There is a conserved LRF sequence motif.
10TM putative phosphate transporter, extracellular tail (PHM7_ext)
Type: Domain

This domain is found in plants and fungi. It represents the C-terminal extracellular domain of the putative phosphate transporter, PHM7 . The three N-terminal TMS are found in family RSN1_TM,

; the cytoplssmic domain is

, and the remaining 7TM region is in

.
Flagellar operon protein YvyF (Flagellar_operon_YvyF)
Type: Family

Proteins in this entry are encoded by a gene that is found in flagellar operons of Bacillus-related organisms. The function is unknown. A tentative assignment as a regulator has been made in some sources.
Accessory Sec system protein Asp3 (Acessory_Sec_prot_Asp3)
Type: Family

Asp3 is part of an accessory SecA2/SecY2 system, which is involved in the export of serine-rich glycoproteins important for virulence in a number of Gram-positive species, including Streptococcus gordonii and Staphylococcus aureus . SecA2/SecY2 system specifically required to export SraP, a serine-rich repeat cell wall protein encoded upstream in the same operon . In Streptococcus gordonii, it may also function in part as chaperones in the early phase of GspB (a serine-rich glycoprotein adhesin) transport .
Integrating conjugative element protein PilL, PFGI-1 (Integr_conj_element_PilL)
Type: Domain

This entry describes the conserved N-terminal region of a variable length protein family associated with laterally transfered regions flanked by markers of conjugative plasmid integration and/or transposition. Most members of the family have the lipoprotein signal peptide motif. A member of the family from a pathogenicity island in Salmonella enterica subsp enterica serovar Dublin strain was designated PilL for nomenclature consistency with a neighbouring gene for the pilin structural protein PilS. However, the species distribution of this protein family tracks much better with markers of conjugal transfer than with markers of PilS-like pilin structure.
Ribosomal natural product, two-chain TOMM family (RNP_Burkhold)
Type: Family

Members of this protein family are found sparsely, mostly in members of the genus Burkholderia. Members often occur as tandem homologous genes, such as BMA_0021 and BMA_0022 in Burkholderia mallei ATCC 23344, or else have a duplication. The genes regularly are encoded near a cyclodehydrogenase/docking protein fusion protein of TOMM (thiazole/oxazole-modified microcins) biosynthetic clusters, suggesting a role in bacteriocin biosynthesis. The role of the putative natural product is unknown, but function as a two-chain bacteriocin is suggested.
Lipoprotein, putative (Lipoprot_put)
Type: Family

Proteins on this entry are usually encoded on the bacterial chromosome, in regions flanked by markers of conjugative transfer and/or transposition. In some cases, however, they are encoded on plasmids. Many are annotated as putative lipoproteins.
KxYKxGKxW signal peptide (KxYKxGKxW)
Type: Conserved_site

This entry describes a novel form of signal peptide that occurs as an N-terminal domain with a recognisable motif, reminiscent of the YSIRK and PEP-CTE forms of signal peptide. This domain tends to occur on long, low-complexity (usually serine-rich and heavily glycosylated) proteins of the Firmicutes, and (as with YSIRK) the majority of these proteins have the LPXTG cell wall-anchoring motif at the C terminus .
Microcyclamide/patellamide bacteriocin family, leader peptide (Microcy/ptell_bactrcn_lead_pep)
Type: Domain

This domain represents the leader peptide found in the microcyclamide and patellamide bacteriocin precursors .
Conserved hypothetical protein CHP03790 (CHP03790)
Type: Family

This entry represents an uncharacterised protein family that occurs only among the roughly 8 percent of prokaryotic species that carry homologues of the integral membrane protein exosortase (see

), a proposed protein-sorting system transpeptidase.
Integrating conjugative element protein, PFL4697-type (Integr_conj_elem_PFL4697-type)
Type: Family

Proteins in this entry are usually encoded on the bacterial main chromosome, in regions flanked by markers of conjugative transfer and/or transposition. Occasionally, however, they are encoded on plasmids such as the Pseudomonas putida TOL plasmid.
Accessory Sec system protein Asp2 (Asp2)
Type: Family

Proteins in this entry form part of an accessory Sec system which is involved in the export of serine-rich glycoproteins important for virulence in a number of Gram-positive species, including Streptococcus gordonii and Staphylococcus aureus . Asp2 directly interacts with Aps1 and Asp3 to form a complex and stabilizes it; this complex is essential for substrate export. Asp2 and Asp3 interact directly with GspB and may function in part as chaperones in the early phase of GspB transport . Moreover, Asp2 acetylates the GlcNAc residues on GspB. Asp1/2/3 complex stimulates the ATPase activity of SecA2 and also affects the export and glycosylation of pneumococcal serine-rich repeat proteins (PrsPs) .
Conserved hypothetical protein CHP03809 (CHP03809)
Type: Family

This protein family contains proteins with a median length of about 175, including a strongly conserved N-terminal region of about 55 amino acids, a conserved extreme C-terminal region of about 15 amino acids, and highly variable sequence in between the two.
Diheme c-type cytochrome SO_2930-like, C-terminal domain (SO_2930-like_C)
Type: Domain

This entry represents the C-terminal region of a group of uncharacterised diheme c-type cytochrome proteins found in the same species as the protein members of (

), usually as the adjacent gene or in a fusion protein. SO_2930 from Shewanella putrefaciens (

,

) and HNE_0200 from Hyphomonas neptunium are included in this entry. Sometimes two members of this family are with a single member of (

). The specific function of these proteins is unknown.
Beta-carotene 15,15'-dioxygenase, Brp/Blh family (Blh_diox)
Type: Family

This prokaryotic integral membrane protein family includes Brp (bacterio-opsin related protein) and Blh (Brp-like protein). Bacteriorhodopsin is a light-driven proton pump consisting of the membrane apoprotein bacterioopsin and a covalently bound retinal cofactor that appears to be derived of beta-carotene. Blh has been shown to cleave beta-carotene to produce two all-trans retinal molecules. It has been suggested that Brp and Blh are similar proteins that catalyze or regulate the conversion of beta-carotene to retinal . Mammalian enzymes with similar enzymatic function are not multiple membrane spanning proteins and are not homologous.
Lipocalin, ApoD type (Lipocalin_ApoD)
Type: Family

This entry represents ApoD-type lipocalins, including retinol-binding protein 4 as well as other retinol-binding proteins. Apolipoprotein D (ApoD) is mainly associated with high-density lipoproteins (HDL) and appears to be able to transport a variety of ligands in a number of different contexts . Insect Lazarillo is an homologue of ApoD .

The lipocalins are a diverse, interesting, yet poorly understood family of proteins composed, in the main, of extracellular ligand-binding proteins displaying high specificity for small hydrophobic molecules . Functions of these proteins include transport of nutrients, control of cell regulation, pheromone transport, cryptic colouration, and the enzymatic synthesis of prostaglandins. For example, retinol-binding protein 4 transfers retinol from the stores in the liver to peripheral tissues .

The crystal structures of several lipocalins have been solved and show a novel 8-stranded anti-parallel β-barrel fold well conserved within the family. Sequence similarity within the family is at a much lower level and would seem to be restricted to conserved disulphides and 3 motifs, which form a juxtaposed cluster that may act as a common cell surface receptor site . By contrast, at the more variable end of the fold are found an internal ligand binding site and a putative surface for the formation of macromolecular complexes . The anti-parallel β-barrel fold is also exploited by the fatty acid-binding proteins, which function similarly by binding small hydrophobic molecules. Similarity at the sequence level, however, is less obvious, being confined to a single short N-terminal motif.
Lipocalin family conserved site (Lipocalin_CS)
Type: Conserved_site

The lipocalins are a diverse, interesting, yet poorly understood family of proteins composed, in the main, of extracellular ligand-binding proteins displaying high specificity for small hydrophobic molecules . Functions of these proteins include transport of nutrients, control of cell regulation, pheromone transport, cryptic colouration, and the enzymatic synthesis of prostaglandins. For example, retinol-binding protein 4 transfers retinol from the stores in the liver to peripheral tissues .

The crystal structures of several lipocalins have been solved and show a novel 8-stranded anti-parallel β-barrel fold well conserved within the family. Sequence similarity within the family is at a much lower level and would seem to be restricted to conserved disulphides and 3 motifs, which form a juxtaposed cluster that may act as a common cell surface receptor site . By contrast, at the more variable end of the fold are found an internal ligand binding site and a putative surface for the formation of macromolecular complexes . The anti-parallel β-barrel fold is also exploited by the fatty acid-binding proteins, which function similarly by binding small hydrophobic molecules. Similarity at the sequence level, however, is less obvious, being confined to a single short N-terminal motif.

This entry represents the Lipocalin conserved site. The sequences of most members of the family, the core or kernal lipocalins, are characterised by three short conserved stretches of residues . Others, the outlier lipocalin group, share only one or two of these. This signature pattern was built around the first, common to all outlier and kernal lipocalins, which occurs near the start of the first β-strand.
ParB-related, ThiF-related cassette, protein E (PRTRC_protein-E)
Type: Domain

PRTRC (ParB-Related, ThiF-Related Cassette) is a novel genetic system characterised by six or seven major proteins, included a ParB homologue and a ThiF homologue. It is often found on plasmids. PRTRC protein E averages about 150 amino acids in length, but the last third contains low-complexity sequence that complicates sequence comparisons. The model in this entry does not include the low-complexity region.
Peptidase aspartic, AF0612 (Peptidase_asp_AF0612)
Type: Family

This entry contains uncharacterised proteins with no known function, however they are predicted to be aspartic peptidases belonging to MEROPS clan AA being related to family

. These proteins resemble retropepsins, pepsin-like proteases of retroviruses such as HIV.
NHPM bacteriocin system secretion protein, HylD (NHPM_bacteriocin_SS_HylD)
Type: Family

This entry represents a protein family which is homologous to the HlyD membrane fusion protein of type I secretion systems. The genes encoding these proteins within prokaryotic genomes are associated with genes encoding a novel class of microcin (small bacteriocin) which has a propeptide region related to nitrile hydratase. The bacteriocin has been designated as Nitrile Hydratase Propeptide Microcin, or NHPM. On this basis, therefore, proteins in this entry are designated as NHPM bacteriocin system secretion proteins. Some, but not all, NHPM-class putative microcins belong to the TOMM (thiazole/oxazole modified microcin) class as assessed by the presence of the scaffolding protein and/or cyclodehydratase in the same gene clusters.
Conjugative transposon, TraK (Conjug_transposon_TraK)
Type: Family

Proteins in this entry are found in a proposed transfer region of a class of conjugative transposons found primarily in the Bacteroides lineage. PSI-BLAST reveals a distant relationship to proteins TrbF and VirB8 in proteobacterial conjugal transfer systems.
Conserved hypothetical protein CHP02171, Fibrobacter succinogenes (CHP02171_FIBSS)
Type: Family

This entry represents a paralogous family of proteins found in the rumen bacterium Fibrobacter succinogenes and closely related species. The proteins average over 900 amino acids in length and are of unknown function, though more than half are predicted lipoproteins.