SII-SWORD/CoKE huggingface dataset:
Bacteriophage lambda, Xis (Q38267) (Phage_lambda_Xis_Q38267)
Type: Family

This entry is represented by Bacteriophage lambda, Xis. This entry overlaps with IPR009750, both representing lambda Xis. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.

This family consists of several hypothetical Escherichia coli and Bacteriophage lambda-like proteins of around 60 residues in length. The function of this family is unknown.
Baculovirus protein AC11 (AcMNPV_AC11)
Type: Family

This family of baculovirus proteins is represented by Autographa californica nuclear polyhedrosis virus (AcMNPV) protein AC11 (Orf11). ac11 is an early gene essential for budded-virus production and occlusion-derived-virus envelopment .
SPATS2-like (SPATS2-like)
Type: Family

This family includes spermatogenesis-associated serine-rich protein 2 (SPATS2) and its paralogue, SPATS2-like protein (SPAT2L) from mammals. SPATS2 is involved in spermatogenesis and likely to be a cytoplasmic RNA-binding protein . SPATS2 is highly expressed in hepatocellular carcinoma (HCC) and may function as an oncogene. It constitutes a novel diagnostic prognostic marker in liver cancer and a potential therapeutic target for the treatment of HCC .
PAM2 motif (PAM2_motif)
Type: Conserved_site

The PABP-interacting motif PAM2 has been identified in various eukaryotic proteins as an important binding site for

. It has been found in a wide range of eukaryotic proteins . Strikingly, this motif appears to occur solely outside of globular domains .
Pes-10 (Pes-10)
Type: Family

This family consists of several Caenorhabditis elegans pes-10 and related proteins. Members of this family are typically around 400 residues in length. The function of this family is unknown.
Protein of unknown function DUF1390 (DUF1390)
Type: Family

This family consists of several Paramecium bursaria chlorella virus 1 (PBCV-1) proteins of around 250 residues in length. The function of this family is unknown.
Protein of unknown function DUF1391 (DUF1391)
Type: Family

This family consists of several Enterobacterial proteins of around 50 residues in length. Members of this family are found in Escherichia coli and Salmonella typhi where they are often known as YdfA. The function of this family is unknown.
YaeQ (YaeQ)
Type: Family

This family consists of several hypothetical bacterial proteins of around 180 residues in length, which are often known as YaeQ. YaeQ is homologous to RfaH, a specialised transcription elongation protein and YaeQ is known to compensate for loss of RfaH function . However, YaeQ does not appear to affect transcription directly and this suppression is most likely due to an indirect effect, so the function of this protein remains unknown .

Structural studies indicate that YaeQ contains a variation of the PD-(D/E)XK nuclease motif found in various endonucleases and enzymes involved in DNA replication, repair, and recombination . This structure, and the high degree of sequence conservation amongst YaeQ and its homologues, suggest that it may be involved in the remodeling or modification of nucleic acid DNA or RNA structures.
Herpesvirus SORF3 (Herpes_SORF3)
Type: Family

This family consists of several SORF3 proteins from the Marek's disease-like viruses (Meleagrid herpesvirus 1, also known as Gallid herpesvirus 2) and other Herpesvirus. Members of this family are around 350 residues in length. The function of this family is unknown.
Protein of unknown function DUF1392 (DUF1392)
Type: Family

This family consists of several hypothetical cyanobacterial proteins of around 150 residues in length. The function of this family is unknown.
ECF transporter, substrate-specific component-like (ECF_substrate-spec-like)
Type: Family

This family consists of several bacterial proteins of around 180 residues in length that appear to be multi-pass membrane proteins. Many family members are functionally uncharacterised. Others appear to be substrate specific components of an energy-coupling factor (ECF) type transport system, such as Thiamine precursor transporter HmpT, which is likely a thiamine precursor-binding protein that interacts with the ECF ABC-transporter complex. Unlike classic ABC transporters, this ECF transporter provides the energy necessary to transport a number of different substrates. The substrates themselves are bound by transmembrane, not extracytoplasmic soluble proteins. .
DNA circulation, N-terminal (DNA_circ_N)
Type: Domain

This entry represents the N terminus (approximately 100 residues) of a number of phage DNA circulation proteins.
Dicarboxylate carrier MatC N-terminal (MatC_N)
Type: Domain

This entry represents the N-terminal region of the bacterial dicarboxylate carrier protein MatC. The MatC protein is an integral membrane protein that could function as a malonate carrier .
CYRIA/CYRIB, Rac1 binding domain (CYRIA/CYRIB_Rac1-bd)
Type: Domain

This domain has been annotated as Rac1-binding domain . It can be found in human CYRIA/CYRIB and at the N terminus of CYFIP1/2 . CYFIP proteins are known RAC1 effectors that stimulate actin polymerization . CYRIA/B are also localised to early macropinosomes and act to modulate their formation by regulating Rac1 signalling . In mice, CYRIB (also known as CYRI or FAM49B) negatively regulates RAC1-driven cytoskeletal remodelling and plays a role in restricting infection mediated by Mycobacterium tuberculosis and Listeria monocytogenes .
Spindle and kinetochore-associated protein 1 (SKA1)
Type: Family

Spindle and kinetochore-associated protein 1 (SKA1, also known as SKA complex subunit 1) is a component of the SKA1 complex (consists of Ska1, Ska2, and Ska3/Rama1), a microtubule-binding subcomplex of the outer kinetochore that is essential for proper chromosome segregation . It is required for timely anaphase onset during mitosis, when chromosomes undergo bipolar attachment on spindle microtubules leading to silencing of the spindle checkpoint . The SKA1 complex is a direct component of the kinetochore-microtubule interface and directly associates with microtubules as oligomeric assemblies. The complex facilitates the processive movement of microspheres along a microtubule in a depolymerisation-coupled manner. SKA1 contains a microtubule-binding domain that interacts with tubulins using multiple contact sites that allow the Ska complex to bind microtubules in multiple modes .
LppX/LprAFG lipoprotein family (LppX/LprAFG)
Type: Family

This entry consists of several lipoproteins mainly from Mycobacterium species, collectively known as the LppX/LprAFG family. Proteins in this entry include:

LprG (

) from Mycobacterium tuberculosis: an immunogenic 27kDa membrane-associated lipoprotein . Expression of the LprG protein is essential for the growth of M. tuberculosis in immunocompetent mice . Purification of LprG showed that it inhibits MHC-II antigen processing in primary human macrophages, providing a mechanism to avoid the host MHC-II-restricted CD4+ T cell response which is considered essential for control of M. tuberculosis infection .

LppX: a lipoprotein required for the translocation of complex lipids to the outer membrane of Mycobacterium tuberculosis. Its structure consists of a U-shaped β-half-barrel with a large hydrophobic cavity .

LprF: a membrane lipoprotein involved in the kdp signal transduction pathway, thought to be the primary response to osmotic stress .

lprA: a lipoprotein agonist of TLR2 that regulates innate immunity and APC function .
Protein of unknown function DUF1397 (DUF1397)
Type: Family

This entry consists of several insect specific 27kDa Haemolymph glycoprotein precursors. The function of this family is unknown .
Uncharacterised protein DUF1398 (DUF1398)
Type: Family

This family consists of several hypothetical bacterial proteins of around 130 residues in length. The function of this family is unknown.
Ureide permease (Ureide_permease)
Type: Family

This entry represents Ureide permease 1-5 from Arabidopsis thaliana and similar proteins from plants and bacteria. UPS transports a wide spectrum of oxo derivatives of heterocyclic nitrogen compounds, including allantoin, uric acid and xanthine, but not adenine. Transport is dependent on glucose and a proton gradient . UPS5, which transports allantoin, has been related to salt and stress tolerance in Arabidopsis plants .
Sortase B family (SrtB)
Type: Family

Members of this transpeptidase family are, in most cases, designated sortase B, product of the srtB gene. This protein shows only distant similarity to the sortase A family, for which there may be several members in a single bacterial genome. Typical SrtB substrate motifs include NAKTN, NPKSS, etc, and otherwise resemble the LPXTG sorting signals recognised by sortase A proteins.
Glycine-rich domain-containing protein-like (GRDP-like)
Type: Family

This entry includes Arabidopsis Glycine-rich domain-containing protein 1 and 2 (GRDP1/2).

Glycine-rich domain-containing proteins (GRDPs) plays a regulatory role in abscisic acid (ABA) signalling and tolerance to abiotic stress during germination. It may be involved in the regulation of the ABI transcriptional factors and in the development of stress responses .
Matrix extracellular phosphoglycoprotein (MEPE)
Type: Family

Matrix extracellular phosphoglycoprotein (also known as Osteoblast/osteocyte factor 45 or osteoregulin) has multiple functions, being involved in cell signalling, mineral homeostasis, and mineralization, as it plays a role in bone mineralization by osteoblasts and cartilage mineralization by chondrocytes . It promotes renal phosphate excretion and inhibits intestinal phosphate absorption .

This entry also includes Ovocleidin-116, the chicken orthologue, which is the major component of the eggshell matrix and is involved in eggshell calcification .
Type IV conjugative transfer system, protein TraL (T4SS_TraL)
Type: Family

This entry represents bacterial TraL proteins. TraL is a predicted peripheral membrane protein involved in bacterial sex pilus assembly . TraL is part of the type IV secretion system for conjugative plasmid transfer . The exact function of TraL is unknown.
SseB protein N-terminal domain (SseB_N)
Type: Domain

This family consists of several SseB proteins which appear to be found exclusively in Enterobacteria. SseB is known to enhance serine-sensitivity in Escherichia coli and is part of the Salmonella pathogenicity island 2 (SPI-2) translocon . This entry contains the presumed N-terminal domain of SseB.
VirC2 (VirC2)
Type: Family

This family consists of several VirC2 proteins which seem to be found exclusively in Agrobacterium species and Rhizobium etli. VirC2 is known to be involved in virulence in Agrobacterium species but its exact function is unclear .
Protein of unknown function DUF1402 (DUF1402)
Type: Family

This family consists of several hypothetical bacterial proteins of around 310 residues in length. Members of this family seem to be found exclusively in alphaproteobacteria. The function of this family is unknown.
Protein of unknown function DUF1403 (DUF1403)
Type: Family

This family consists of several hypothetical bacterial proteins of around 320 residues in length. Members of this family are mainly found in Rhizobium and Agrobacterium species. The function of this family is unknown.
Protein of unknown function DUF1404 (DUF1404)
Type: Family

This family consists of several archaeal proteins of around 180 residues in length. Members of this family seem to be found exclusively in Sulfolobus tokodaii and Sulfolobus solfataricus. The function of this family is unknown.
Protein of unknown function DUF1405 (DUF1405)
Type: Family

This family consists of several bacterial and related archaeal protein of around 180 residues in length. The function of this family is unknown.
Splicing factor 3B subunit 5/RDS3 complex subunit 10 (SF3b5/RDS3-10)
Type: Family

This family consists of several eukaryotic splicing factor 3B subunit 5 (SF3b5) proteins. SF3b5 is a 10kDa subunit of the splicing factor SF3b. SF3b associates with the splicing factor SF3a and a 12S RNA unit to form the U2 small nuclear ribonucleoproteins complex. SF3b5 and SF3b14b are also thought to facilitate the interaction of U2 with the branch site . Also included in this entry is RDS3 complex subunit 10, another protein involved in mRNA splicing .
SNURF family (SNURF)
Type: Family

This family consists of several mammalian SNRPN upstream reading frame (SNURF) proteins. SNURF or RPF4 is a RING-finger protein and a coregulator of androgen receptor-dependent transcription. It has been suggested that SNURF is involved in the regulation of processes required for late steps of spermatid maturation .
Protein of unknown function DUF1408 (DUF1408)
Type: Family

This family consists of several hypothetical Lactococcus lactis and related phage proteins of around 75 residues in length. The function of this family is unknown.
Domain of unknown function DUF1410 (DUF1410)
Type: Domain

This entry represents a conserved domain, approximately 100 residues long, multiple copies of which are sometimes found within hypothetical Ureaplasma parvum proteins of unknown function, as well as related species.
Domain of unknown function DUF1411 (DUF1411)
Type: Domain

This domain is sometimes repeated within some eukaryotic Babesia proteins of unknown function, including

from B.bovis. It covers almost the full length of the protein in sequences from the archaeal Sulfolobus, such as

.
Modifier of rudimentary, Modr (Mod_r)
Type: Domain

This entry represents a conserved region approximately 150 residues long within a number of eukaryotic proteins that show homology with Drosophila melanogaster Modifier of rudimentary (Mod(r)) proteins. The N-terminal half of Mod(r) proteins is acidic, whereas the C-terminal half is basic , and both of these regions are represented in this family.
Centromere protein J, C-terminal domain (CENPJ_C_dom)
Type: Domain

This entry represents a C-terminal domain found in members of the T complex protein 10 family. This domain contains unusual G repeats . Centromere protein J (also known as Centrosomal-P4.1-associated-protein, CPAP), a member of the TCP10 family, plays an important role in cell division and centrosome function by participating in centriole duplication . It inhibits microtubule nucleation from the centrosome and depolymerises taxol-stabilised microtubules . It may also be involved in the control of centriolar-microtubule growth by acting as a regulator of tubulin release . T-complex is involved in spermatogenesis in mice .

This domain, also known as TCP and G-box, is essential for the tethering of pericentriolar material (PCM), the principle site for microtubule nucleation and anchoring. It adopts an extended single-layer antiparallel β-sheet configuration . Mutations in this region are associated with primary microcephaly .
Protein of unknown function DUF1412 (DUF1412)
Type: Family

This family consists of several Caenorhabditis elegans proteins of around 70-75 residues in length. The function of this family is unknown.
Orthoreovirus membrane fusion p10 (Orthoreo_P10)
Type: Family

This family consists of several Orthoreovirus membrane fusion protein p10 sequences. p10 is thought to be a multifunctional protein that plays a key role in virus-host interaction .
Baculovirus late expression factor 10 (Baculo_LEF-10)
Type: Family

This family consists of several Baculovirus specific late expression factor 10 (LEF-10) sequences. LEF-10 is thought to be a late expressed structural protein although its exact function is unknown .
Light regulated Lir1 (Lir1)
Type: Family

This family consists of several plant specific light regulated Lir1 proteins. Lir1 mRNA accumulates in the light, reaching maximum and minimum steady-state levels at the end of the light and dark period, respectively. Plants germinated in the dark have very low levels of lir1 mRNA, whereas plants germinated in continuous light express lir1 at an intermediate but constant level. It is thought that lir1 expression is controlled by light and a circadian clock . Lir1 interacts with LEAF-TYPE Ferredoxin-NADP(+) oxidoreductase (LFNR), an essential chloroplast enzyme functioning in the last step of photosynthetic linear electron transfer, and forms a thylakoid protein complex with LFNR, TIC62 and TROL .
Uncharacterised protein family UPF0352 (UPF0352)
Type: Family

This family consists of several hypothetical bacterial proteins of around 70 residues in length. Members of this family are often referred to as YejL. The function of this family is unknown.
Protein of unknown function DUF1415 (DUF1415)
Type: Family

This family consists of several hypothetical bacterial proteins of around 180 residues in length. The function of this family is unknown.
Protein of unknown function, Gam-like (Gam-like)
Type: Family

The Gam protein, originally characterised in Bacteriophage Mu, protects linear double stranded DNA from exonuclease degradation
in vitro
and
in vivo
. This protein is also found in many bacterial species as part of a suspected prophage. Further studies have shown that Gam is a functional counterpart of the eukaryotic Ku protein, which has key roles in DNA repair and in certain transposition events.
Gam displays DNA binding characteristics remarkably similar to those of human Ku . In addition, Gam can interfere with Ty1 retrotransposition in Saccharomyces cerevisiae (Baker's yeast). These data reveal structural and functional parallels between bacteriophage Gam and eukaryotic Ku and suggest that their functions have been evolutionarily conserved .

This family consists of several hypothetical bacterial and phage proteins of around 180 residues in length. The function of these proteins is not currently known, but they are related to the host-nuclease inhibitor protein Gam.
Hyaluronidase, bacterial (Hyaluronidase_bac)
Type: Family

This family consists of several phage associated hyaluronidase proteins (

) which are mostly from Streptococcus pyogenes and its bacteriophages. The substrate of hyaluronidase is hyaluronic acid, a sugar polymer composed of alternating N-acetylglucosamine and glucuronic acid residues. Hyaluronic acid is found in the ground substance of human connective tissue and the vitreous of the eye and also is the sole component of the capsule of group A streptococci. The capsule has been shown to be an important virulence factor of this organism by virtue of its ability to resist phagocytosis. Production by S. pyogenes of both a hyaluronic acid capsule and hyaluronidase enzymatic activity capable of destroying the capsule is an interesting, yet-unexplained, phenomenon .
Hematopoietic cell signal transducer (HCST)
Type: Family

Hematopoietic cell signal transducer (HCST, also known as DAP10) is a transmembrane adaptor that associates with an activation receptor, NKG2D, which is found on NK and subsets of T cells. The ligands for this receptor include MHC class I chain-related (MIC) protein A and protein B and UL16-binding proteins . In activated mouse natural killer (NK) cells, the NKG2D receptor associates with two intracellular adaptors, DAP10 and DAP12, which trigger phosphatidyl inositol 3 kinase (PI3K) and Syk family protein tyrosine kinases, respectively. It has been suggested that the DAP10-PI3K pathway is sufficient to initiate NKG2D-mediated killing of target cells .
Protein of unknown function DUF1419 (DUF1419)
Type: Family

This family consists of several bacterial proteins of around 110 residues in length. Members of this family seem to be specific to Agrobacterium species and to Rhizobium loti (Mesorhizobium loti). The function of this family is unknown.
Type III secretion protein, LcrG (T3SS_LcrG_PcrG)
Type: Family

LcrG is found in type III secretion operons, along with LcrR, H and V. LcrG is a negative regulator for secretion of Yersinia outer-membrane proteins (Yops) by blocking the secretion apparatus from the inner membrane . Also known as PcrG in Pseudomonas, the protein is believed to make a 1:1 complex with PcrV (LcrV) . Mutations in LcrG cause premature secretion of effector proteins into the medium .
Rhoptry-associated protein 1, plasmodium (RAP1_Plasmodium)
Type: Family

This family consists of several rhoptry-associated protein 1 (RAP-1) sequences which appear to be specific to Plasmodium falciparum .
Proacrosin binding sp32 (Proacrosin-bd)
Type: Family

This family consists of several mammalian specific proacrosin binding protein sp32 sequences. sp32 is a sperm specific protein, which is known to bind with 55- and 53kDa proacrosins and the 49kDa acrosin intermediate. The exact function of sp32 is unclear, it is thought however that the binding of sp32 to proacrosin may be involved in packaging the acrosin zymogene into the acrosomal matrix . During the activation of the boar proacrosin/acrosin system, the expression of sp32 is upregulated and its tyrosine phosphorylation levels is increased .
NADH:ubiquinone oxidoreductase, subunit NDUFB4 (NADH_UbQ_OxRdtase_NDUFB4_su)
Type: Family

This family contains the accessory subunit of complex I NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4 NDUFB4, not involved in catalysis .
Protein of unknown function DUF1422 (DUF1422)
Type: Family

This family consists of several hypothetical bacterial proteins of around 120 residues in length. The function of this family is unknown.
VirE2 (VirE2)
Type: Family

This family consists of several VirE2 proteins which seem to be specific to Agrobacterium tumefaciens and Rhizobium etli. VirE2 is known to interact, via its C terminus, with VirD4. A. tumefaciens transfers oncogenic DNA and effector proteins to plant cells during the course of infection. Substrate translocation across the bacterial cell envelope is mediated by a type IV secretion (TFS) system composed of the VirB proteins, as well as VirD4, a member of a large family of inner membrane proteins implicated in the coupling of DNA transfer intermediates to the secretion machine. VirE2 is therefore thought to be a protein substrate of a type IV secretion system which is recruited to a member of the coupling protein superfamily .
Nematode resistance protein-like HSPRO1, N-terminal (HSPRO1_N)
Type: Domain

This entry represents the N terminus (approximately 180 residues) of plant HSPRO1, which is believed to confer resistance to nematodes . Proteins containing this domain also include HSPRO2, which is involved in basal resistance .
Putative replication protein DUF1424 (DUF1424)
Type: Family

Members of this family seem to be found mainly in Halobacteria. The function of this family is unknown. This protein is probably a replication protein due to conservation of functional motifs.
Movement and RNA silencing protein (MP)
Type: Family

This family consists of several Babuvirus proteins of around 120 residues in length. Proteins in this family include movement and RNA silencing protein (also known as MP) from Banana bunchy top virus. MP acts as a suppressor of RNA-mediated gene silencing, also known as post-transcriptional gene silencing (PTGS), a mechanism of plant viral defense that limits the accumulation of viral RNAs. It transports viral genome to neighbouring plant cells directly through plasmosdesmata, without any budding. The movement protein allows efficient cell to cell propagation, by bypassing the host cell wall barrier .
Protein of unknown function DUF1427 (DUF1427)
Type: Family

This family consists of several bacterial proteins of around 100 residues in length. The function of this family is unknown.
Phytoreovirus S7 (Phytoreo_S7)
Type: Family

This family consists of several Phytoreovirus S7 proteins which are thought to be viral core proteins .
Protein of unknown function DUF1428 (DUF1428)
Type: Family

This family consists of several hypothetical bacterial and one archaeal sequence of around 120 residues in length. The function of this family is unknown.