SII-SWORD/CoKE huggingface dataset:
Senescence/spartin-associated, C-terminal (Senescence/spartin_C)
Type: Domain

This is the AAA ATPase domain found at the C-terminal of plant senescence-associated proteins and spartin. In Hemerocallis, petals have a genetically based program that leads to senescence and cell death approximately 24 hours, after the flower opens, and it is believed that senescence proteins produced around that time have a role in this program . This domain is also found at the C-terminal of Spartin, a protein from higher vertebrates associated with endosomal trafficking and microtubule dynamics . Spartin functions presynaptically with endocytic adaptor Eps15 to regulate synaptic growth and function. Mutations in human spartin gene cause Troyer syndrome, a hereditary spastic paraplegia . This AAA ATPase domain similar to other AAA proteins contain an α/β nucleotide-binding domain (NBD) and a smaller four-helix bundle domain (HBD) . Uniquely among AAA structures, spastin has two helices (N-terminal α1 and C-terminal α11) that embrace the NBD .
Protein FAM210A/B-like domain (FAM210A/B-like_dom)
Type: Domain

This domain is found in mitochondrial proteins, including FAM210A (and its homologues) and B, which contain a transmembrane peptide . Its function is not clear. FAM210A, a protein essential in maintaining skeletal muscle structure and strength , interacts with mitochondrial translation elongation factor EF-Tu and promotes mitochondrial protein expression. In FAM210A, this domain is responsible for binding EF-Tu . FAM210B plays a role in erythroid differentiation and is involved in cell proliferation and tumor cell growth suppression . This domain is also present in the uncharacterised protein C106.07c from fission yeast and putative N-terminal acetyltransferase 2 from Baker's yeast.
Protein of unknown function DUF1280 (DUF1280)
Type: Family

This family represents a conserved region approximately 200 residues long within a number of proteins of unknown function that seem to be specific to Caenorhabditis elegans.
Bacteriophage T4, Gp30.7 (Phage_T4_Gp30_7)
Type: Family

This family consists of several phage Gp30.7 proteins of 121 residues in length. Family members seem to be exclusively from the T4-like viruses. The function of this family is unknown.
P13 protein, Citrus tristeza virus (P13_Citrus_tristeza_virus)
Type: Family

This entry represents the 13kDa P13 protein from Citrus tristeza virus (CTV) strains. CTV, a member of the closterovirus group, is one of the more complex single-stranded RNA viruses . The function of the P13 protein is unknown.
Glucitol operon activator (Glucitol_operon_activator)
Type: Family

This family consists of several glucitol operon activator (GutM) proteins. Expression of the glucitol (gut) operon in Escherichia coli is regulated by an unusual, complex system, which consists of an activator (encoded by the gutM gene) and a repressor (encoded by the gutR gene) in addition to the cAMP-CRP complex (CRP, cAMP receptor protein). Synthesis of the mRNA, which initiates at the promoter specific to the gutR gene, occurs within the gutM gene. Expressional control of the gut operon appears to occur as a consequence of the antagonistic action of the products of the autogenously regulated gutM and gutR genes .
Domain of unknown function DUF1281 (DUF1281)
Type: Domain

This entry describes a domain of unkown function found generally at the N-terminal of YubA and YubB in enterobacteriaceae. This domain is mostly found in Escherichia coli, Salmonella typhimurium and Shigella species. This domain is usually found in association with

.

YubA and YubB have not been fully functionally characterised. YubB was identified as undecaprenyl diphosphate phosphatase (UPPP) due to its association with cell wall synthesis and bacitracin resistance when disrupted. YubA was inferred to be a transporter, possibly related to cell wall synthesis, based on its predicted membrane protein structure and its genomic association with the UPPP gene. These experiments were done using transposon mutagenesis .
Diacylglycerol glucosyltransferase, N-terminal (Diacylglyc_glucosyltr_N)
Type: Domain

This entry represents a conserved region of approximately 180 residues found towards the N terminus of a number of glycosyltransferases, such as plant chloroplastic monogalactosyldiacylglycerol synthases and bacterial diacylglycerol glucosyltransferases .
Putative replisome organiser, C-terminal (Rep_Org_C)
Type: Domain

This entry represents the C terminus (approximately 100 residues) of a putative replisome organiser protein in Lactococcus bacteriophages .
Mastadenovirus E4/Orf3 (Mastadenovirus_E4/Orf3)
Type: Family

This family consists of several Mastadenovirus E4 ORF3 proteins. Early proteins E4 ORF3 and E4 ORF6 have complementary functions during viral infection. Both proteins facilitate efficient viral DNA replication, late protein expression, and prevention of concatenation of viral genomes. A unique function of E4 ORF3 is the reorganisation of nuclear structures known as PML oncogenic domains (PODs). The function of these domains is unclear, but PODs have been implicated in a number of important cellular processes, including transcriptional regulation, apoptosis, transformation, and response to interferon .
Protein of unknown function DUF1283 (DUF1283)
Type: Family

This family consists of several hypothetical proteins of around 115 residues in length, which seem to be specific to Enterobacteria. The function of the family is unknown.
Special lobe-specific silk SSP160 (SSP160)
Type: Family

This family consists of several special lobe-specific silk protein SSP160 sequences which appear to be specific to Chironomus (Midge) species.
Protein of unknown function DUF1284 (DUF1284)
Type: Family

This family consists of several hypothetical bacterial and archaeal proteins of around 130 residues in length. The function of this family is unknown, although it is thought that they may be iron-sulphur binding proteins.
Selenoprotein S (Selenoprotein_S)
Type: Family

This family consists of several mammalian selenoprotein S (SelS) sequences. SelS is a plasma membrane protein and is present in a variety of tissues and cell types. These proteins are involved in the degradation process of misfolded endoplasmic reticulum (ER) luminal proteins which participate in the transfer of misfolded proteins from the ER to the cytosol, where they are destroyed by the proteasome in a ubiquitin-dependent manner . They probably serve as a linker between DER1, which mediates the retro-translocation of misfolded proteins into the cytosol, and the ATPase complex VCP, which mediates the translocation and ubiquitination.
EURL protein (EURL_prot)
Type: Family

This family consists of several animal EURL proteins. EURL is preferentially expressed in chick retinal precursor cells as well as in the anterior epithelial cells of the lens at early stages of development. EURL transcripts are found primarily in the peripheral dorsal retina, i.e., the most undifferentiated part of the dorsal retina. EURL transcripts are also detected in the lens at stage 18 and remain abundant in the proliferating epithelial cells of the lens until at least day 11. The distribution pattern of EURL in the developing retina and lens suggest a role before the events leading to cell determination and differentiation .
Protein of unknown function DUF1286 (DUF1286)
Type: Family

This family consists of several hypothetical archaeal proteins of around 120 residues in length. Most proteins in this group are found in the family Sulfolobaceae. The function of this protein family is unknown.
Protein of unknown function DUF1287 (DUF1287)
Type: Family

This family consists of several hypothetical bacterial proteins of around 200 residues in length. The function of this family is unknown.
Membrane protein GlpM/YdgC (GlpM/YdgC)
Type: Family

This family consists of several bacterial membrane proteins, including GlpM Pseudomonas aeruginosa and YdgC from
E. coli
. GlpM may play a role in alginate biosynthesis . The function of inner membrane protein YdgC is not clear .
Bacteriophage A118-like, holin/antiholin (Phage_A118_holin/antiholin)
Type: Family

This entry represents the Bacteriophage A118-like, holin/antiholin protein. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.

An alternative isoform exists that is thought to function as an antiholin by counteracting the aggregation of the holin molecules. The isoforms differ by only 2 residues at the N terminus .

Holins form large oligomeric flexible pores in the cytoplasmic membranes of bacteria to allow the endolysins to gain access to the cell wall, where they exert their actions by cleaving various bonds in the peptidoglycan polymer and inducing cell death. These proteins and its corresponding genes have been identified in a wide variety of Gram-negative and Gram-positive bacteria and their phages .
Protein of unknown function DUF1290 (DUF1290)
Type: Family

This family consists of several bacterial small basic proteins of around 100 residues in length. The function of this family is unknown.
Uncharacterised protein family UPF0473 (UPF0473)
Type: Family

This family consists of several hypothetical bacterial proteins of around 90 residues in length. The function of this family is unknown.
Vibrio phage Vf33, Vpf117 (Vibrio_phage_Vf33_Vpf117)
Type: Family

This entry is represented by Vibrio phage Vf33, Vpf117. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.

This family consists of several bacterial and phage proteins of around 115 residues in length. The function of this family is unknown.
Uncharacterised protein family PsiA (Uncharacterised_PsiA)
Type: Family

This family consists of several Enterobacterial PsiA proteins. The function of PsiA is unknown although it is thought that it may affect the generation of an SOS signal in Escherichia coli .
Resistin-like molecule hormone family (RELM)
Type: Family

RELMs, secreted proteins with roles including insulin resistance and the activation of inflammatory processes, are also known as found in inflammatory zone (FIZZ), and include four members in mouse (RELM-alpha/FIZZ1/HIMF, RELM-beta/FIZZ2, Resistin/FIZZ3, and RELM-gamma/FIZZ4) and two members in human (resistin and RELM-beta). RELMs are potentially implicated in a wide range of physiological and pathological processes including obesity-associated diabetes, cardiovascular system function, cancer development and metastasis .

There are significant differences between human and rodent RELMs with respect to gene and protein structure, differential gene regulation, different tissue distribution profiles, and insulin resistance induction. Resistin appears to convey insulin resistance in rodents, and to instigate inflammatory processes in humans. In the pathophysiology of obesity-associated diabetes, mouse resistin is secreted by adipocytes and increases hepatic gluconeogenesis, thereby promoting insulin resistance, human resistin is secreted by macrophages and may play a role through inflammatory contributions .
Regulator of RNA terminal phosphate cyclase (RtcR)
Type: Domain

RtcR is a sigma54-dependent enhancer binding protein that activates transcription of the rtcBA operon. The product of the rtcA gene is an RNA 3 -terminal phosphate cyclase . This domain is found at the N terminus of the RtcR sequence. RtcR, and other sigma54-dependent activators, contain

in the central region of the protein sequence.
Ferroportin-1 (Ferroportin-1)
Type: Family

This entry represents the Solute carrier family 40 member 1 (SLC40A) family of proteins, also known as Ferroportin 1 (or simply ferroportin (FPN), the major iron transporter key in cellular and systemic iron levels balance. In mammals, it mediates the absorption of dietary iron by transporting ferrous iron across the basolateral surface of duodenal enterocytes and can also recycle iron from hepatocytes and macrophages. FPN is also involved in iron transfer between maternal and fetal circulation . FPN synthesis is transcriptionally regulated by cellular hypoxia, iron and heme concentrations, and inflammatory signalling, while cell surface FPN is negatively regulated by hepcidin, which, under elevated serum iron levels, it blocks iron transport and induces FPN ubiquitination, internalization, and degradation . Structural studies in Bdellovibrio bacteriovorous suggest that the putative substrate-binding site is localized deep in the N-terminal domain and demonstrated that Ca facilitates a conformational change critical to the transport cycle . In humans, mutations in this transporter leads to nonclassical ferroportin disease (FD), a form of hereditary hemochromatosis .
Mo-dependent nitrogenase, C-terminal (Mo-dep_Nase_C)
Type: Domain

This entry represents the C terminus (approximately 80 residues) of a number of bacterial Mo-dependent nitrogenases. These are involved in nitrogen fixation in cyanobacteria .
Rex DNA-binding, C-terminal domain (Rex_DNA-bd_C_dom)
Type: Domain

This entry represents the C terminus (approximately 30 residues) of a number of Rex proteins. These are redox-sensing repressors that appear to be widespread among Gram-positive bacteria . They modulate transcription in response to changes in cellular NADH/NAD
(+)
redox state. Rex is predicted to include a pyridine nucleotide-binding domain (Rossmann fold), and residues that might play key structural and nucleotide binding roles are highly conserved.
GBF-interacting protein 1, N-terminal (GIP1_N)
Type: Domain

This entry represents the N-terminal domain of GBF1-interacting protein 1 (GIP1, AT3G13222) from Arabidopsis. GIP1 may act as a coactivator that regulates transcription factors involved in lateral organ development of plants, such as bZIP transcription factors and LBD18 .
IMP biosynthesis enzyme PurP, C-terminal (IMP_biosynth_PurP_C)
Type: Domain

The last two steps of
de novo
purine biosynthesis are:

conversion of 5-aminoimidazole-4-carboxamide-1-beta-D-ribofuranosyl 5'-monophosphate (AICAR) to 5-formaminoimidazole-4-carboxamide-1-beta-D-ribofuranosyl 5'-monophosphate (FAICAR)

conversion of FAICAR to inosine5'-monophopsphate (IMP)

In bacteria and eukaryotes, these steps are catalysed by the well-characterised bifunctional enzyme PurH . Archaea do not appear to posses PurH, however, and perform these reactions by a different mechanism . In archaea, step i) is catalysed by the well-conserved PurP protein, while step ii) is catalysed by the PurO enzyme in some (though not all) species .

This entry represents the C-terminal domain of PurP, which is homologous to the ATP-GRASP fold and thus may be involved in ATP-binding. It is almost always found in association with

.
O-acyltransferase WSD1, C-terminal (O-acyltransferase_WSD1_C)
Type: Domain

This entry represents the C terminus (approximately 170 residues) of wax ester synthase/diacylglycerol acyltransferases (WS/DGATs), predominantly from bacteria and plants, including O-acyltransferase WSD1 which is involved in cuticular wax biosynthesis . They catalyse the condensation of a fatty alcohol and a fatty acyl-Coenzyme A (acyl-CoA) and they can also catalyse the transesterification of acyl-CoAs with diacylglycerols. These are bifunctional enzymes that share low overall sequence similarity but all WS/DGATs share a conserved HHXXXDG motif, which is also found in other acyltransferases .
YjiK/CarP (YjiK/CarP)
Type: Family

This entry represents a family of hypothetical bacterial proteins that may be regulated by SdiA, a member of the LuxR family of transcriptional regulators . This entry includes the uncharacterised protein YjiK in Escherichia coli and the calcium-regulated β-propeller protein CarP in Pseudomonas .
Pop1, N-terminal (Pop1_N)
Type: Domain

This entry represents a conserved region approximately 150 residues long located towards the N terminus of the POP1 subunit that is common to both the RNase MRP and RNase P ribonucleoproteins (

) . These RNA-containing enzymes generate mature tRNA molecules by cleaving their 5' ends. This is a short N-terminal domain consisting of a small helical core and a long α-helix , which is enriched with positively charged residues involved in pre-tRNA substrate recognition .
TMEM70 family (TMEM70)
Type: Family

TMEM70 is a family of proteins essential for assembly of the mitochondrial proton-transporting ATP synthase complex within the inner mitochondrial membrane .
Predicted 3-demethylubiquinone-9 3-methyltransferase (3_dmu_93_MTrfase)
Type: Family

This entry contains a number of predicted bacterial and archaeal 3-demethylubiquinone-9 3-methyltransferases, which have a conserved region of approximately 100 residues. In some proteins this region occurs more than once.
NifT/FixU (NifT)
Type: Family

This family consists of several NifT and FixU bacterial proteins. The function of NifT is unknown although it is thought that the protein may be involved in biosynthesis of the FeMo cofactor of nitrogenase although perturbation of nifT expression in Klebsiella pneumoniae has only a limited effect on nitrogen fixation .
BAALC (BAALC)
Type: Family

This entry represents the mammalian BAALC proteins. BAALC (brain and acute leukaemia, cytoplasmic) is highly conserved among mammals, but is absent from lower organisms. Two isoforms are specifically expressed in neuroectoderm-derived tissues, but not in tumours or cancer cell lines of non-neural tissue origin. It has been shown that blasts from a subset of patients with acute leukaemia greatly overexpress eight different BAALC transcripts, resulting in five protein isoforms. Among patients with acute myeloid leukaemia, those overexpressing BAALC show distinctly poor prognosis, pointing to a key role of the BAALC products in leukaemia. It has been suggested that BAALC is a gene implicated in both neuroectodermal and hematopoietic cell functions .
Galactose-3-O-sulfotransferase (Gal-3-0_sulfotransfrase)
Type: Family

This family consists of several animal galactose-3-O-sulphotransferases, including GAL3ST1-4. GAL3ST1 (also known as Cst, cerebroside sulfotransferase) is responsible for the biosynthesis of two types of sulfoglycolipids, sulfatide (HSO3-3-galactosylceramide) and seminolipid (HSO3-3-monogalactosylalkylacylglycerol), in mammals. It catalyses the sulfation of membrane glycolipids and seems to prefer beta-glycosides at the non-reducing termini of sugar chains attached to a lipid moiety. It also catalyses the synthesis of galactosylceramide sulfate (sulfatide), a major lipid component of the myelin sheath and of monogalactosylalkylacylglycerol sulfate (seminolipid), present in spermatocytes .
Micro-fibrillar-associated protein 1, C-terminal (MFAP1_C)
Type: Domain

This entry represents the C terminus (approximately 300 residues) of eukaryotic micro-fibrillar-associated protein 1, which is a component of elastin-associated microfibrils in the extracellular matrix .
Replication P-like (P-like)
Type: Family

This entry represents a family of proteins from tailed bacteriophages and proteobacterial prophages, including Bacteriophage lambda replication protein P, also known as Helicase loader. This protein promotes replication of the phage chromosome by recruiting a key component of the cellular replication machinery to the viral origin. Specifically, it delivers one or more molecules of Escherichia coli DnaB helicase to a nucleoprotein structure formed by the lambda O initiator at the lambda replication origin .
Protein of unknown function DUF1304 (DUF1304)
Type: Family

This family consists of several hypothetical bacterial proteins of around 120 residues in length. The function of this family is unknown.
Involucrin 2 (Involucrin2)
Type: Domain

This domain represents a conserved region approximately 60 residues long, multiple copies of which are found within eukaryotic involucrin, and which is rich in glutamine and glutamic acid residues. Involucrin forms part of the insoluble cornified cell envelope (a specialised protective barrier) of stratified squamous epithelia .
Myoviridae, GpU (Myoviridae_GpU)
Type: Family

This family consists of several bacterial and phage proteins of around 130 residues in length which seem to be related to the bacteriophage P2 GpU protein (

) which is thought to be involved in tail assembly .
Protein of unknown function DUF1307 (DUF1307)
Type: Family

This family consists of several hypothetical bacterial proteins of around 150 residues in length. Some family members are described as putative lipoproteins but the function of the family is unknown.
Thioredoxin-like ferredoxin (Aim32/Apd1-like)
Type: Family

This entry includes proteins from fungi, plants and bacteria. Proteins in this entry contain a ferredoxin-like fold. They are predicted ferredoxins, which are iron-sulfur (Fe-S) proteins that may play a role in redox sensing and electron transfer . Some members appear to have sucrolytic activity . The putative active site of the ferredoxin-like domain of the enzyme contains two cysteines and two histidines for possible binding to iron-sulfur clusters, compared to four cysteines present in the active site of ferredoxin .

Two budding yeast proteins, Aim32 and Apd1, are included in this entry. Apd1 is an Fe-S protein and is involved in cellular defense against hydroxyurea . It is required for normal localisation of actin patches in budding yeasts . The function of Aim32 is not clear.
BAT2, N-terminal (BAT2_N)
Type: Domain

This entry represents the N terminus (approximately 200 residues) of the proline-rich protein BAT2 (also known as PRRC2A). BAT2 is similar to other proteins with large proline-rich domains, such as some nuclear proteins, collagens, elastin, and synapsin .
Lysozyme inhibitor LprI-like, N-terminal (LprI-like_N)
Type: Domain

This domain is found in uncharacterised bacterial proteins and towards the N-terminal part of lipoprotein LprI from Mycobacterium. The function of this domain is not known. LprI binds to and inhibits macrophage lysozyme, which may aid bacterial survival .
Protein EARLY FLOWERING 4 domain (EARLY_FLOWERING_4_dom)
Type: Domain

Protein EARLY FLOWERING 4 is a component of the central CCA1/LHY-TOC1 feedback loop in the circadian clock that promotes clock accuracy and is required for sustained rhythms in the absence of daily light/dark cycles .

This domain forms an α-helical homodimer in ELF4 proteins.
Curlin associated (Curlin_rpt)
Type: Repeat

This entry represents a bacterial repeated motif of around 30 residues in length. These repeats are often found in multiple copies in the curlin proteins CsgA and CsgB. Curli fibres are thin aggregative surface fibres, connected with adhesion, which bind laminin, fibronectin, plasminogen, human contact phase proteins, and major histocompatibility complex (MHC) class I molecules. Curli fibres are coded for by the csg gene cluster, which is comprised of two divergently transcribed operons. One operon encodes the csgB, csgA, and csgC genes, while the other encodes csgD, csgE, csgF, and csgG. The assembly of the fibres is unique and involves extracellular self-assembly of the curlin subunit (CsgA), dependent on a specific nucleator protein (CsgB). CsgD is a transcriptional activator essential for expression of the two curli fibre operons, and CsgG is an outer membrane lipoprotein involved in extracellular stabilisation of CsgA and CsgB .
Hs1pro-1, C-terminal (Hs1pro-1_C)
Type: Domain

This entry represents the C terminus (approximately 270 residues) of a number of plant Hs1pro-1 proteins, which are believed to confer nematode resistance .
VirC1 (VirC1)
Type: Family

This family consists of several bacterial VirC1 proteins. In Agrobacterium tumefaciens, a cis-active 24-base-pair sequence adjacent to the right border of the T-DNA, called overdrive, stimulates tumour formation by increasing the level of T-DNA processing. It is thought that the virC operon, which enhances T-DNA processing probably, does so because the VirC1 protein interacts with overdrive. It has now been shown that the virC1 gene product binds to overdrive but not to the right border of T-DNA .