SII-SWORD/CoKE huggingface dataset:
PKD/Chitinase domain (PKD/Chitinase_dom)
Type: Domain

The PKD (Polycystic Kidney Disease) domain was first identified in the Polycystic Kidney Disease protein, polycystin-1 (PDK1 gene), and contains an Ig-like fold consisting of a β-sandwich of seven strands in two sheets with a Greek key topology, although some members have additional strands . Polycystin-1 is a large cell-surface glycoprotein involved in adhesive protein-protein and protein-carbohydrate interactions; however it is not clear if the PKD domain mediates any of these interactions.
ABC transporter, permease F420-0 (ABC_transptr_permease_F420-0)
Type: Family

This small clade of ABC-type transporter permease protein components is found as a three gene cassette along with a periplasmic substrate-binding protein (

) and an ATPase (

). The organisms containing this cassette are all Actinobacteria and all contain numerous genes requiring the coenzyme F420. This model was defined based on five such organisms, four of which are lacking all F420 biosynthetic capability save the final side-chain polyglutamate attachment step (via the gene cofE:

). In Jonesia denitrificans DSM 20603 and marine actinobacterium PHSC20C1 this cassette is in an apparent operon with the cofE gene and, in PHSC20C1, also with an F420-dependent glucose-6-phosphate dehydrogenase (

). Based on these observations we propose that this permease protein is a component of a F420-0 (that is, F420 lacking only the polyglutamate tail) transporter.
C-type cytochrome, methanol metabolism-related (C-typ_cyt_methanol_metab-rel)
Type: Family

This entry represents a c-type cytochrome related to (but excluding) cytochrome c-555 of Methylococcus capsulatus. Members contain four invariant Cys residues, including two from a heme-binding motif shared with c-555, and two others.
Quinolinate phosphoribosyl transferase, N-terminal (Quinolinate_PRibosylTrfase_N)
Type: Domain

Quinolinate phosphoribosyl transferase (QPRTase) or nicotinate-nucleotide pyrophosphorylase

is involved in the
de novo
synthesis of NAD in both prokaryotes and eukaryotes. It catalyses the reaction of quinolinic acid with 5-phosphoribosyl-1-pyrophosphate (PRPP) in the presence of Mg
2+
to give rise to nicotinic acid mononucleotide (NaMN), pyrophosphate and carbon dioxide . Unlike

, this domain also includes the molybdenum transport system protein ModD.
ATP:guanido phosphotransferase, N-terminal (ATP-guanido_PTrfase_N)
Type: Domain

This entry represents the N-terminal domain of ATP:guanido phosphotransferase, which has an all-α fold consisting of an irregular array of 6 short helices .

ATP:guanido phosphotransferases are a family of structurally and functionally related enzymes that reversibly catalyse the transfer of phosphate between ATP and various phosphogens. The enzymes belonging to this family include:

Glycocyamine kinase (

), which catalyses the transfer of phosphate from ATP to guanidoacetate.

Arginine kinase (

), which catalyses the transfer of phosphate from ATP to arginine.

Taurocyamine kinase (

), an annelid-specific enzyme that catalyses the transfer of phosphate from ATP to taurocyamine. One member is Smc74, a cercaria-specific enzyme from Schistosoma mansoni .

Lombricine kinase (

), an annelid-specific enzyme that catalyses the transfer of phosphate from ATP to lombricine.

Creatine kinase (

) (CK) , which catalyses the reversible transfer of high energy phosphate from ATP to creatine, generating phosphocreatine and ADP.

Creatine kinase plays an important role in energy metabolism of vertebrates. There are at least four different, but very closely related, forms of CK. Two isozymes, M (muscle) and B (brain), are cytosolic, while the other two are mitochondrial. In sea urchins there is a flagellar isozyme, which consists of the triplication of a CK-domain. A cysteine residue is implicated in the catalytic activity of these enzymes and the region around this active site residue is highly conserved.
ATP:guanido phosphotransferase, catalytic domain (ATP-guanido_PTrfase_cat)
Type: Domain

This entry represents the C-terminal catalytic domain of ATP:guanido phosphotransferase that consists of two similar subdomains, the common core of which comprises two β-α-β2-α repeats . The substrate binding site is located in the cleft between N and C-terminal subdomains, but most of the catalytic residues are found in the larger C-terminal subdomain .

Eukaryotic phosphagen kinases consist of a small, ~100-residue, α-helical N-terminal domain and a larger, ~250-residue, C-terminal α/β-saddle domain in which many key residues involved in catalysis are found. The N-terminal domain undergoes significant conformational movements during catalysis, closing down on the catalytic pocket. It is involved in dimer formation. Bacterial phosphagen kinases have the large C-terminal domain seen in eukaryotic phosphagen kinases but lack the N-terminal domain .

ATP:guanido phosphotransferases are a family of structurally and functionally related enzymes that reversibly catalyse the transfer of phosphate between ATP and various phosphogens. The enzymes belonging to this family include:

Glycocyamine kinase (

), which catalyses the transfer of phosphate from ATP to guanidoacetate.

Arginine kinase (

), which catalyses the transfer of phosphate from ATP to arginine.

Taurocyamine kinase (

), an annelid-specific enzyme that catalyses the transfer of phosphate from ATP to taurocyamine. One member is Smc74, a cercaria-specific enzyme from Schistosoma mansoni .

Lombricine kinase (

), an annelid-specific enzyme that catalyses the transfer of phosphate from ATP to lombricine.

Creatine kinase (

) (CK) , which catalyses the reversible transfer of high energy phosphate from ATP to creatine, generating phosphocreatine and ADP.

Creatine kinase plays an important role in energy metabolism of vertebrates. There are at least four different, but very closely related, forms of CK. Two isozymes, M (muscle) and B (brain), are cytosolic, while the other two are mitochondrial. In sea urchins there is a flagellar isozyme, which consists of the triplication of a CK-domain. A cysteine residue is implicated in the catalytic activity of these enzymes and the region around this active site residue is highly conserved.
ATP:guanido phosphotransferase active site (ATP-guanido_PTrfase_AS)
Type: Active_site

This entry represents the conserved region surrounding a cysteine residue in the C-terminal catalytic domain that is implicated in the catalytic activity of these enzymes. C-terminal catalytic domain of ATP:guanido phosphotransferase, which is comprised of a duplication where the common core consists of two β-α-β2-α repeats . The substrate binding site is located in the cleft between N and C-terminal domains, but most of the catalytic residues are found in the larger C-terminal domain .

ATP:guanido phosphotransferases are a family of structurally and functionally related enzymes that reversibly catalyse the transfer of phosphate between ATP and various phosphogens. The enzymes belonging to this family include:

Glycocyamine kinase (

), which catalyses the transfer of phosphate from ATP to guanidoacetate.

Arginine kinase (

), which catalyses the transfer of phosphate from ATP to arginine.

Taurocyamine kinase (

), an annelid-specific enzyme that catalyses the transfer of phosphate from ATP to taurocyamine. One member is Smc74, a cercaria-specific enzyme from Schistosoma mansoni .

Lombricine kinase (

), an annelid-specific enzyme that catalyses the transfer of phosphate from ATP to lombricine.

Creatine kinase (

) (CK) , which catalyses the reversible transfer of high energy phosphate from ATP to creatine, generating phosphocreatine and ADP.

Creatine kinase plays an important role in energy metabolism of vertebrates. There are at least four different, but very closely related, forms of CK. Two isozymes, M (muscle) and B (brain), are cytosolic, while the other two are mitochondrial. In sea urchins there is a flagellar isozyme, which consists of the triplication of a CK-domain. A cysteine residue is implicated in the catalytic activity of these enzymes and the region around this active site residue is highly conserved.
Prion/Doppel protein, beta-ribbon domain (Prion/Doppel_prot_b-ribbon_dom)
Type: Domain

This entry represents the C-terminal β-ribbon domain found in prion proteins and the prion-like Doppel proteins . This domain has a β-α-β-α(2) structure that contains an antiparallel β-ribbon.

Prion protein (PrP-c) is a small glycoprotein found in high quantity in the brain of animals infected with certain degenerative neurological diseases, such as sheep scrapie and bovine spongiform encephalopathy (BSE), and the human dementias Creutzfeldt-Jacob disease (CJD) and Gerstmann-Straussler syndrome (GSS). PrP-c is encoded in the host genome and is expressed both in normal and infected cells. During infection, however, the PrP-c molecule become altered (conformationally rather than at the amino acid level) to an abnormal isoform, PrP-sc. In detergent-treated brain extracts from infected individuals, fibrils composed of polymers of PrP-sc, namely scrapie-associated fibrils or prion rods, can be evidenced by electron microscopy. The precise function of the normal PrP isoform in healthy individuals remains unknown. Several results, mainly obtained in transgenic animals, indicate that PrP-c might play a role in long-term potentiation, in sleep physiology, in oxidative burst compensation (PrP can fix four Cu2+ through its octarepeat domain), in interactions with the extracellular matrix (PrP-c can bind to the precursor of the laminin receptor, LRP), in apoptosis and in signal transduction (costimulation of PrP-c induces a modulation of Fyn kinase phosphorylation) .

The normal isoform, PrP-c, is anchored at the cell membrane, in rafts, through a glycosyl phosphatidyl inositol (GPI); its half-life at the cell surface is 5 h, after which the protein is internalised through a caveolae-dependent mechanism and degraded in the endolysosome compartment. Conversion between PrP-c and PrP-sc occurs likely during the internalisation process.
Porphobilinogen deaminase, dipyrromethane cofactor binding site (Porphobilin_deaminase_cofac_BS)
Type: Binding_site

This entry represents the region around a cysteine residues that is conserved in porphobilinogen deaminases from various prokaryotic and eukaryotic sources. The sulphur atom of this cysteine residue has been shown in the Escherichia coli enzyme (gene hemC) to be bound to the dipyrromethane cofactor . Porphobilinogen deaminase covalently binds a dipyrromethane cofactor to which the PBG subunits are added in a stepwise fashion. Porphobilinogen deaminase has a three-domain structure. Domains 1 (N-terminal) and 2 are duplications with the same structure, resembling the transferrins and periplasmic binding proteins. The dipyrromethane cofactor is covalently linked to domain 3 (C-terminal), but is bound by extensive salt-bridges and hydrogen-bonds within the cleft between domains 1 and 2, at a position corresponding to the binding sites for small-molecule ligands in the analogous proteins . The enzyme has a single catalytic site, and the flexibility between domains is thought to aid elongation of the polypyrrole product in the active-site cleft of the enzyme.
Circadian clock protein, KaiC, archaea (Circ_KaiC_arc)
Type: Family

This entry represents a rather narrowly distributed archaeal protein family in which members have a single copy of the KaiC domain. This stands in contrast to the circadian clock protein KaiC itself, with two copies of the domain. Members are expected to have weak ATPase activity, by homology to the autokinase/autophosphorylase KaiC itself.
Relaxin (Relaxin)
Type: Family

The insulin/IGF/relaxin superfamily is an ancient family of functionally diverse proteins . The 3D structures of a number of family members have been determined . The fold comprises two polypeptide chains (A and B) linked by two disulphide bonds: all share a conserved arrangement of four cysteines in their A chain, the first of which is linked by a disulfide bond to the third, while the second and fourth are linked by interchain disulfide bonds to cysteines in the B chain.

This family includes:

Insulin and insulin-like proteins

Relaxin and prorelaxin

Insect prothoracicotropic hormone (bombyxin)

Insulin-like growth factors (IGF1 and IGF2)

Mammalian Leydig cell-specific insulin-like peptide (gene INSL3)

Invertebrates insulin-related peptides (IRPs)
Protein import receptor MAS20, metazoan (MAS20_rcpt_metazoan)
Type: Family

Virtually all mitochondrial precursors are imported via the same mechanism : precursors first bind to receptors on the mitochondrial surface, then insert into the translocation channel in the outer membrane. Many outer-membrane proteins participate in the early stages of import, 4 of which (MAS20, MAS22, MAS37 and MAS70) are components of the receptor. MAS20, which forms a subcomplex with MAS22, seems to interact with most or all mitochondrial precursors, suggesting that the protein binds directly to mitochondrial targeting sequences. The MAS37 and MAS70 components also form a subcomplex, the 2 subcomplexes possibly binding via their trans-membrane (TM) regions -the TM region of MAS70 promotes oligomerisation of attatched protein domains and shares sequence similarity with the TM region of MAS20 .
Neurohypophysial hormone, conserved site (Neurohypophysial_hormone_CS)
Type: Conserved_site

Oxytocin (or ocytocin) and vasopressin are small (nine amino acid residues), structurally and functionally related neurohypophysial peptide hormones. Oxytocin causes contraction of the smooth muscle of the uterus and of the mammary gland while vasopressin has a direct antidiuretic action on the kidney and also causes vasoconstriction of the peripheral vessels. Like the majority of active peptides, both hormones are synthesized as larger protein precursors that are enzymatically converted to their mature forms. Peptides containing this conserved site are also found in birds, fish, reptiles and amphibians (mesotocin, isotocin, valitocin, glumitocin, aspargtocin, vasotocin, seritocin, asvatocin, phasvatocin), in worms (annetocin), octopi (cephalotocin), locust (locupressin or neuropeptide F1/F2) and in molluscs (conopressins G and S) .
Translation initiation factor 2, gamma subunit (TIF2_gsu)
Type: Family

This entry represents the gamma subunit of archaeal translation initiation factor 2, it is found in all known archaea. eIF-2 functions in the early steps of protein synthesis by forming a ternary complex with GTP and initiator tRNA .
Flagellar export ATPase FliI, clade 2 (FliI_clade2)
Type: Family

Members of this protein family are the FliI protein of bacterial flagellum systems. FliI is an ATPase that acts to drive protein export for flagellar biosynthesis . The most closely related family is the YscN family of bacterial type III secretion systems. This entry represents one (of three) segment of the FliI family tree. These have been modeled separately in order to exclude the type III secretion ATPases more effectively.
Flagellum-specific ATP synthase FliI, clade 3 (FliI_clade3)
Type: Family

This family represent the bacterial flagellum-specific ATP synthase, FliI, which is needed for flagellar assembly. FliI is part of the flagellar type III protein export apparatus acting as an ATPase to drive protein export for flagellar biosynthesis . When FliI is not engaged in flagellar protein export, FliH, another flagellar type III protein export apparatus protein, functions as a negative regulator to prevent FliI from hydrolysing ATP . It has been suggested that the N terminus of FliI interacts with FliH, while the the C-terminal domain of FliI possesses the ATPase catalytic function . The structure of the N-terminally truncated variant of FliI lacking the first 18 residues have been determinded .

This entry represents one (of three) segment of the FliI family tree.
Uncharacterised protein MJ0570, ATP-binding (MJ0570_ATP-bd)
Type: Family

This entry represents possible ATP binding proteins from Archaea, including the uncharacterised protein MJ0570 from Methanocaldococcus jannaschii and PF0828 from Pyrococcus furiosus (

,

).
Diphthamide synthesis Dph2, archaea (Dph2_arc)
Type: Family

Archaeal and eukaryotic translation elongation factor 2 contain a unique posttranslationally modified histidine residue called diphthamide, the target of the diphtheria toxin .
Alanine-tRNA ligase, archaea (Ala-tRNA_lgiase_arc)
Type: Family

Alanine-tRNA ligase (also known as alanyl-tRNA synthetase) (

) is an alpha4 tetramer that belongs to class IIc.

Alanine-tRNA ligase catalyzes the attachment of alanine to tRNA(Ala) in a two-step reaction: alanine is first activated by ATP to form Ala-AMP and then transferred to the acceptor end of tRNA(Ala). It also edits incorrectly charged Ser-tRNA(Ala) and Gly-tRNA(Ala) via its editing domain.

This family of alanine-tRNA ligases is limited to the archaea.

The aminoacyl-tRNA synthetases (also known as aminoacyl-tRNA ligases) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction . These proteins differ widely in size and oligomeric state, and have limited sequence homology . The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric . Class II aminoacyl-tRNA synthetases share an anti-parallel β-sheet fold flanked by α-helices , and are mostly dimeric or multimeric, containing at least three conserved regions . However, tRNA binding involves an α-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan, valine, and some lysine synthetases (non-eukaryotic group) belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, phenylalanine, proline, serine, threonine, and some lysine synthetases (non-archaeal group), belong to class-II synthetases. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c .
Conserved hypothetical protein CHP03684 (CHP03684)
Type: Family

This universal archaeal protein contains a C-terminal PUA domain possibly associated with RNA-binding.
Cyclic dehypoxanthine futalosine synthase (Cyclic_DHFL_synthase_mqnC)
Type: Family

Members of this protein family are involved in menaquinone biosynthesis by an alternate pathway via futalosine .
Aminodeoxyfutalosine synthase (MqnE)
Type: Family

Members of this protein family are aminofutalosine synthases (MqnE,

) and are involved in menaquinone biosynthesis. The Thermus thermophilus family member, MqnE, has been experimentally characterised as a a radical SAM enzyme that catalyses the addition of the adenosyl radical to the double bond of 3-[(1 -carboxyvinyl)oxy]benzoic acid .
Lipid kinase YegS (Lip_kinase_YegS)
Type: Family

Members of this protein family are designated YegS, an apparent lipid kinase family in the Proteobacteria. The crystal structure of YegS has been reported and been shown to be a lipid kinase with phosphatidylglycerol kinase activity. The crystal structure reveals a two-domain protein with significant structural similarity to a family of NAD kinases. The active site is located in the interdomain cleft formed by four conserved sequence motifs. Surprisingly, the structure reveals a novel metal binding site composed of residues conserved in most lipid kinases .
ABC transporter, LPXTG-anchor lipoprotein, actinobacteria (ABC_LPXTG_lipo_actinobac)
Type: Family

Members of this protein family are ABC transporter permease subunits as identified by

, but additionally contain the Actinobacterial insert domain described by

. Some homologues (lacking the insert) have been described as transporters of manganese or of chelated iron. Members of this family typically are found along with an ATP-binding cassette protein, a permease, and an LPXTG-anchored protein with two or three copies of the

insert that occurs just once in this protein family.
Surface-anchored repeat, actinobacteria (Surface-anchored_actinobac)
Type: Repeat

This entry describes a region that occurs from one to three times in proteins from Actinobacteria, some of which have LPXTG-type sortase recognition motifs for covalent attachment to the Gram-positive cell wall. The region is now recognized as a "choice-of-anchor" domain, since multiple members can be found anchored by sortases (e.g. LPXTG proteins) or exosortases (e.g. PEP-CTERM proteins).
Rickettsia palindromic element RPE2 (RPE2)
Type: Domain

This entry describes a family, family 2, of Rickettsia palindromic elements (RPE2). The elements spread within a genome as selfish genetic elements, inserting into genes creating additional coding regions that do not disrupt the reading frame. This model finds RPE-encoded regions in several Rickettsial species and, so far, no where else.
Rickettsia palindromic element RPE3 (RPE3)
Type: Domain

This entry represents family 3 of Rickettsia palindromic elements (RPE3).

These elements spread within a genome as selfish genetic elements, inserting into genes creating additional coding regions that do not disrupt the reading frame (ORF), but are expressed as part of the proteins encoded by them . Members of this entry are found in Rickettsial species.
Rickettsia palindromic element 5 (RPE5)
Type: Domain

This entry represents family 5 of Rickettsia palindromic elements (RPE5).

These elements spread within a genome as selfish genetic elements, inserting into genes creating additional coding regions that do not disrupt the reading frame (ORF), but are expressed as part of the proteins encoded by them . Members of this entry are found in Rickettsial species.
Rickettsia palindromic element RPE4 (RPE4)
Type: Domain

This entry represents Rickettsia palindromic element RPE4, a palindromic element found in several Rickettsial species. The elements spread within a genome as selfish genetic elements, inserting into genes creating additional coding regions that do not disrupt the reading frame.
Conserved hypothetical protein CHP03788 (CHP03788)
Type: Family

Members of this protein family are restricted to the Proteobacteria. Each contains a C-terminal sortase-recognition motif, transmembrane domain, and basic residues cluster at the the C terminus, and is encoded adjacent to a sortase gene. This protein is frequently the only sortase target in its genome, which is as unusual its occurrence in Gram-negative rather than Gram-positive genomes. Many bacteria with this system are marine. In addition to the LPXTG signal, members carry a vault protein inter-alpha-trypsin inhibitor domain (

) and a von Willebrand factor type A domain (

).
Parallel beta-helix repeat-2 (Para_beta_helix_rpt-2)
Type: Repeat

This model represents a tandem pair of an approximately 22-amino acid (each) repeat homologous to the β-strand repeats that stack in a right-handed parallel β-helix in the periplasmic C-5 mannuronan epimerase, AlgA, of Pseudomonas aeruginosa. A homology domain consisting of a longer tandem array of these repeats is described in the SMART database as CASH (SM00722), and is found in many carbohydrate-binding proteins and sugar hydrolases. A single repeat is represented by SM00710. This TIGRFAMs model represents a flavor of the parallel β-helix-forming repeat based on prokaryotic sequences only in its seed alignment, although it also finds many eukaryotic sequences .