SII-SWORD/CoKE huggingface dataset:
Peptidase M76, ATP23 (Peptidase_M76_ATP23)
Type: Family

Mitochondrial inner membrane protease ATP23 has two roles in the assembly of mitochondrial ATPase. Firstly, it acts as a protease that removes the N-terminal 10 residues of mitochondrial ATPase CF(0) subunit 6 (ATP6) at the intermembrane space side. Secondly, it is involved in the correct assembly of the membrane-embedded ATPase CF(0) particle, probably mediating association of ATP6 with the subunit 9 ring .
MICOS complex subunit MIC26/MIC27 (MIC26/MIC27)
Type: Family

This entry includes MICOS complex subunit Mic26 from fungi and animals. Mammalian MIC26 and its paralogue, MIC27, can also be found in this entry. However, this entry does not include budding yeast Mic27.
mRNA decay factor PAT1 domain (PAT1_dom)
Type: Domain

This entry represents a domain found in Pat1 and its homologues.

Pat1 is involved in translational repression and enhanced mRNA decay. It is part of the Lsm1-7-Pat1 complex that plays a role in activation of deadenylation-dependent decapping in the 5' to 3' pathway and in the protection of mRNA 3' ends .

There are two Pat1 homologues in vertebrates, Pat1a and Pat1b, in contrast to the single protein in yeast and invertebrates. The maternally expressed Pat1a protein acts as a translational repressor, while Pat1b functions in mRNA decay in somatic cells. Pat1b is localised to P-body and is a nucleocytoplasmic shuttling protein that may perform various nuclear functions upstream of their multiple posttranscriptional regulatory roles in the cytoplasm .
Nuclear envelope phosphatase-regulatory subunit 1 (NEP1-R1)
Type: Family

Nuclear envelope phosphatase 1-regulatory subunit 1 (NEP1-R1), formerly known as TMEM188, functions in the lipin activation pathway . NEP1R1 forms a complex with the phosphatase CTDNEP1. The complex dephosphorylates and may activate phosphatidate phosphatases Lipin-1 and -2, which catalyse the conversion of phosphatidic acid to diacylglycerol.
Transmembrane protein 26 (Transmembrane_26)
Type: Family

The function of this family of transmembrane proteins has not, as yet, been determined.
Meckelin (Meckelin)
Type: Family

Meckelin (also known as MKS3) is part of the tectonic-like complex which is required for tissue-specific ciliogenesis and may regulate ciliary membrane composition . It is involved in centrosome migration to the apical cell surface during early ciliogenesis. It is required for ciliary structure and function, including a role in regulating length and appropriate number through modulating centrosome duplication . It is essential for endoplasmic reticulum-associated degradation (ERAD) of surfactant protein C (sftpc) .
Intermembrane space protein MIX23 (MIX23)
Type: Family

The intermembrane space protein MIX23 regulates or stabilises the mitochondrial protein import machinery and is specifically up-regulated under stress conditions. It is critical for the efficient import of proteins into the mitochondrial matrix, particularly if the function of the translocase of the inner membrane 23 is compromised. MIX23, also known as Caffeine-induced death protein 2 (Cid2), is evolutionarily conserved and a homologue of the human protein CCDC58 .
Osteopetrosis-associated transmembrane protein 1 precursor (Osteopetrosis-assoc_TM_1)
Type: Family

Osteopetrosis-associated transmembrane protein 1 (OSTM1) is required for osteoclast and melanocyte maturation and function. Mutations in OSTM1 give rise to autosomal recessive osteopetrosis, also called autosomal recessive Albers-Schonberg disease .
NADH:ubiquinone oxidoreductase, NDUFB5/SGDH subunit (NADH_UbQ_OxRdtase_B5_su)
Type: Family

Members of this family mediate the transfer of electrons from NADH to the respiratory chain. The immediate electron acceptor for the enzyme is believed to be ubiquinone, the reaction that occurs being: NADH + ubiquinone = NAD(+) + ubiquinol .
NADH dehydrogenase 1, beta subcomplex, subunit 6 (NADH_DH_b-subcmplx_su6)
Type: Family

The NADH dehydrogenase [ubiquinone] complex performs the first stage of electron transfer from NADH to the respiratory chain. This entry represents an accessory subunit that is not thought to be involved in catalysis .
Prp31 C-terminal (Prp31_C)
Type: Domain

This is the C-terminal domain of the pre-mRNA processing factor Prp31. Prp31 is required for U4/U6*U5 tri-snRNP formation . In humans this protein has been linked to autosomal dominant retinitis pigmentosa .
Cytochrome B561-related (Cytochrome_B561-rel)
Type: Family

Members of this family include cytochrome B561, as well as various other putative, uncharacterised proteins.
Golgin subfamily A member 5 (Golgin_subfamily_A_member_5)
Type: Family

This entry represents a family of proteins involved in maintaining Golgi structure. They stimulate the formation of Golgi stacks and ribbons, and are involved in intra-Golgi retrograde transport. Two main interactions have been characterised: one with RAB1A that has been activated by GTP-binding and another with isoform CASP of CUTL1 .
Phosphatidylinositol 4,5-bisphosphate 4-phosphatase (PtdIns-P2-Ptase)
Type: Family

Phosphatidylinositol-4,5-bisphosphate 4-phosphatases type I and type II, also known as transmembrane proteins 55B and 55A, are two metazoan enzymes that catalyse the hydrolysis of PtdIns-4,5-P(2) to phosphatidylinositol-5-phosphate (PtdIns-5-P) .
Coiled-coil domain-containing protein 149 (CC149)
Type: Family

Members of this family have been annotated as being coiled-coil domain-containing protein 149, however they currently have no known function.
Oxidoreductase-like, N-terminal (Oxidoreductase-like_N)
Type: Domain

This entry represents the N-terminal domain of various oxidoreductase-like proteins whose exact function is, as yet, unknown.
LSM12, anticodon-binding domain (LSM12_ABD)
Type: Domain

This domain of approximately 100 residues is conserved from plants to humans. It is an anticodon-binding domain of a prolyl-tRNA synthetase . It is found in Lms12 and homologues. Lsm12 is a putative RNA-binding and regulation protein that might be involved in mRNA degradation or tRNA splicing . Recently, it was demonstrated that it binds nicotinic acid adenine dinucleotide phosphate (NAADP) that confers NAADP sensitivity to the two pore channel complex (TPCs) by acting as TPC accessory protein necessary for NAADP-evoked Ca2 release . Therefore, further studies of the potential crosstalk between NAADP signaling and RNA regulation are required.
Cytochrome b-c1 complex subunit 10, fungi (Cytochrome_b-c1_su10_fun)
Type: Family

This entry represents subunit 10 of the cytochrome b-c1 complex (also known as the ubiquinol-cytochrome c reductase complex or complex III). This complex is located on the inner mitochondrial membrane and it couples electron transfer from ubiquinol to cytochrome. Subunit 10 is required for stable association of the iron-sulphur protein with the complex .
N-alpha-acetyltransferase 25, NatB auxiliary subunit (NAA25_NatB_aux_su)
Type: Family

This entry represents the N-alpha-acetyltransferase 25, NatB auxiliary subunit (NAA25) which is the non-catalytic subunit of the N-terminal acetyltransferase B complex (NatB). NAA25 forms a horseshoe-like deck to hold specifically the catalytic subunit Naa20. The NatB complex catalyses the acetylation of the amino-terminal methionine residue of all proteins beginning with Met-Asp or Met-Glu and of some proteins beginning with Met-Asn or Met-Met . In Saccharomyces cerevisiae (Baker's yeast) this subunit is called MDM20 and in Schizosaccharomyces pombe (Fission yeast) it is called Arm1. NatB acetylates the Tpm1 protein and regulates and tropomyosin-actin interactions. This subunit is required by the NatB complex for the N-terminal acetylation of Tpm1 .
Uncharacterised protein family, transmembrane-17 (Uncharacterised_TM-17)
Type: Family

This entry represents a 100 amino acid region from a family of proteins that is predicted to be a transmembrane region but its function is not known.
Integral membrane protein SYS1-related (Integral_membrane_SYS1-rel)
Type: Family

Members of this family are integral membrane proteins involved in protein trafficking between the late Golgi and endosome. They may also serve as a receptor for ADP-ribosylation factor-related protein 1 (ARFRP1) . Sys1p is a small integral membrane protein with four predicted transmembrane domains that localises to the Trans Golgi network TGN in yeast and human cells .
Nucleolar protein 12 (Nucleolar_protein_12)
Type: Family

Nop12 is a novel nucleolar protein required for pre-large subunit rRNA processing and in yeast normal rates of cell growth at low temperatures .
snRNA-activating protein complex subunit 1 (SNAPC1)
Type: Family

Members of this family are part of the SNAPc complex required for the transcription of both RNA polymerase II and III small-nuclear RNA genes. They bind to the proximal sequence element (PSE), a non-TATA-box basal promoter element common to these 2 types of genes. Furthermore, they also recruit TBP and BRF2 to the U6 snRNA TATA box. SNAPc consists of at least four stably associated subunits, SNAP43, SNAP45, SNAP50, and SNAP190. None of the three small subunits can bind to the PSE on their own .
Large ribosomal subunit protein mL41 (Ribosomal_mL41)
Type: Family

This entry represents the large ribosomal subunit protein mL41, previously known as L27 in yeast and L41 in animals. mL41 is a component of the mitochondrial ribosome (mitoribosome), a dedicated translation machinery responsible for the synthesis of mitochondrial genome-encoded proteins, including at least some of the essential transmembrane subunits of the mitochondrial respiratory chain. The mitoribosomes are attached to the mitochondrial inner membrane and translation products are cotranslationally integrated into the membrane . Animal members of this family are also involved in apoptosis and cell cycle regulation . This group also includes some uncharacterised plant proteins.
Exonuclease V (EXOV)
Type: Family

In Saccharomyces cerevisiae (Baker's yeast), Exo5 is a single strand DNA specific 5'-exonuclease, which is involved in mitochondrial DNA replication and recombination. It has the capacity to slide across 5' double-stranded DNA or 5'RNA sequences and resumes cutting two nucleotides downstream of the double-stranded-to-single-stranded junction or RNA-to-DNA junction, respectively . It degrades single-stranded, but not double-stranded, DNA from the 5'-end, and the products are dinucleotides, except the 3'-terminal tri- and tetranucleotides, which are not degraded. The initial hydrolytic cut of exonuclease V on the dephosphorylated substrate produces a mixture of dinucleoside monophosphates and trinucleoside diphosphates . Exo5 is specific for single-stranded DNA and does not hydrolyze RNA .
Essential protein Yae1, N-terminal (Essential_protein_Yae1_N)
Type: Domain

This entry represents proteins found in the N-terminal region of the essential protein Yae1. Proteins containing this domain include ORAOV1 (Oral cancer-overexpressed protein 1) and YAE1 . Their function is not clear. In Saccharomyces cerevisiae, Lto1 (ORAOV1 homologue) forms a complex with Rli1 and Yae1, which relieves the toxic effects of reactive oxygen species (ROS) on biogenesis and function of the ribosome .
Large ribosomal subunit protein mL40 (Ribosomal_mL40)
Type: Family

This entry represents the large ribosomal subunit protein mL40, previously known as L28 in yeast and L40 in mammals. Members of this family are components of the mitochondrial ribosome (mitoribosome), a dedicated translation machinery responsible for the synthesis of mitochondrial genome-encoded proteins, including at least some of the essential transmembrane subunits of the mitochondrial respiratory chain. The mitoribosomes are attached to the mitochondrial inner membrane and translation products are cotranslationally integrated into the membrane . Mature mitochondrial ribosomes consist of a small (37S) and a large (54S) subunit. The 37S subunit contains at least 33 different proteins and 1 molecule of RNA (15S). The 54S subunit contains at least 45 different proteins and 1 molecule of RNA (21S) .

Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites . About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits.

Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome .
Ubiquitin-conjugating enzyme E2-binding protein (UBQ-conj_enz_E2-bd_prot)
Type: Family

This entry consists of E3 ubiquitin-protein ligases which accept ubiquitin from specific E2 ubiquitin-conjugating enzymes, and transfer it to substrates, generally promoting their degradation by the proteasome .
Transcription elongation factor Eaf, N-terminal (Tscrpt_elong_fac_Eaf_N)
Type: Domain

This entry represents the N-terminal domain of ELL-associated factor (Eaf) proteins, which act as transcriptional transactivators of ELL and ELL2 RNA Polymerase II (Pol II) transcriptional elongation factors . Eaf proteins form a stable heterodimer complex with ELL proteins to facilitate the binding of RNA polymerase II to activate transcription elongation. ELL and EAF1 are components of Cajal bodies, which have a role in leukemogenesis . EAF1 also has the capacity to interact with ELL1 and ELL2. The N terminus of approx 120 of EAF1 has a region of high serine, aspartic acid, and glutamic acid residues .
ABC-type uncharacterised transport system (ABC_transp_unknown)
Type: Domain

This domain is found in various prokaryotic intra-flagellar transport proteins involved in gliding motility, as well as in several hypothetical proteins.
Biotin-protein ligase, N-terminal (Biotin-prot_ligase_N)
Type: Domain

The function of this structural domain is unknown. It is found to the N terminus of the biotin protein ligase catalytic domain . Biotin protein ligase carries out the post-translational modification of specific proteins by the attachment of biotin. It acts on various carboxylases such as acetyl-CoA-carboxylase, pyruvate carboxylase, propionyl CoA carboxylase, and 3-methylcrotonyl CoA carboxylase.
Beta-propeller domain-containing family (Beta_propeller_containing)
Type: Family

This entry consists of predicted secreted proteins containing a C-terminal β-propeller domain distantly related to WD-40 repeats.
Virulence-associated protein D / CRISPR associated protein Cas2 (Virulence_VapD/CRISPR_Cas2)
Type: Family

This entry represents members of the family of Cas2, one of the first four protein families found to be associated with prokaryotic genomes containing multiple CRISPR elements. CRISPR systems protect against invasive nucleic acid sequences, including phage. Cas2 proteins have been characterised as either endoribonuclease (for ssRNA) or endodeoxyribonuclease (for dsDNA), depending on the system to which the Cas2 belongs . The cas genes usually are found near the palindromic repeats. It's worth noting that there is a distinct branch of the Cas2 family

showing a very low level of sequence identity .

The structural subunit of Cas2, belongs to the VapD family of interferases. The interferase catalytic site is intact in the majority of the Cas2 proteins but is disrupted in some, and is not required for spacer acquisition .

The CRISPR-Cas system is a prokaryotic defence mechanism against foreign genetic elements. The key elements of this defence system are the Cas proteins and the CRISPR RNA.

This entry also includes the endoribonuclease VapD . These proteins are defined by a conserved region found at the N terminus of the VapD protein .
ATP adenylyltransferase, C-terminal (ATP_adenylylTrfase_C)
Type: Domain

Diadenosine 5',5'''-P-1,P-4-tetraphosphate (Ap4A) and related diadenosine oligoposphates such as Ap3A are important intracellular and extracellular signalling molecules in prokaryotes and eukaryotes . They are implicated in the regulation of many vital celluar functions including stress response, cell division and apoptosis. Synthesis primarily occurs via aminoacyl-tRNA synthetases adding the AMP moiety of an aminoacyl-AMP to an acceptor nucleotide, and is an inevitable byproduct of protein synthesis. The concentration of these compounds must thus be controlled both to ensure the proper regulation of various celluar processes, but also to prevent their buildup to potentially toxic levels.

This domain is found in a group of ATP adenylyltransferases found in bacteria and lower eukaryotes which catalyse the interconversion of Ap4A to ATP and ADP . While these enzymes are thought to act primarily to break down Ap4A, there is evidence to suggest that in some circumstances they may also act in a biosynthetic role. Some variability in substrate range is apparent eg the cyanobacterial enzyme can also utilise Ap3A as a substrate, while the Saccharomyces enzymes apparently cannot.
Protein of unknown function DUF2065 (DUF2065)
Type: Family

This entry represents a protein found in various prokaryotic proteins, and has no known function.
Protein of unknown function DUF2067 (DUF2067)
Type: Family

This family of archaeal proteins, have no known function.
Domain of unknown function DUF2070, membrane (DUF2070_membrane)
Type: Domain

This domain of unknown function is found in various bacterial and archaeal hypothetical proteins, as well as in prokaryotic polyketide synthase.
Protein of unknown function DUF2080, transposon-encoded (DUF2080_transposon-encoded)
Type: Family

This entry, found in various hypothetical archaeal proteins, has no known function.
Protein of unknown function DUF2085, transmembrane (DUF2085_TM)
Type: Family

This entry, found in various hypothetical prokaryotic proteins, has no known function.
Protein of unknown function DUF2092, periplasmic (DUF2092)
Type: Family

This entry represents various hypothetical prokaryotic proteins of unknown function.
Protein of unknown function DUF2097 (DUF2097)
Type: Family

This domain, found in various hypothetical prokaryotic proteins, has no known function.
Protein of unknown function DUF2098 (DUF2098)
Type: Family

This family of proteins have no known function.
Energy-converting hydrogenase subunit EhaL (EhaL)
Type: Family

[NiFe] hydrogenases function in H2 metabolism in a variety of microorganisms, enabling them to use H2 as a source of reducing equivalent under aerobic and anaerobic conditions [NiFe] hydrogenases consist of two subunits, hydrogenase large and hydrogenase small. The large subunit contains the binuclear [NiFe] active site, while the small subunit binds at least one [4Fe-4S] cluster .

Energy-converting [NiFe] hydrogenases (or [NiFe]-hydrogenase-3-type) form a distinct group within the [NiFe] hydrogenase family . Members of this subgroup include:

Hydrogenase 3 and 4 (Hyc and Hyf) from Escherichia coli

CO-induced hydrogenase (Coo) from Rhodospirillum rubrum

Mbh hydrogenase from Pyrococcus furiosus

Eha and Ehb hydrogenases from Methanothermobacter species

Ech hydrogenase from Methanosarcina barkeri

Energy-converting [NiFe] hydrogenases are membrane-bound enzymes with a six-subunit core: the large and small hydrogenase subunits, plus two hydrophilic proteins and two integral membrane proteins. Their large and small subunits show little sequence similarity to other [NiFe] hydrogenases, except for key conserved residues coordinating the active site and [FeS] cluster. However, they show considerable sequence similarity to the six-subunit, energy-conserving NADH:quinone oxidoreductases (complex I), which are present in cytoplasmic membranes of many bacteria and in inner mitochondrial membranes. However, the reactions they catalyse differ significantly from complex I. Energy-converting [NiFe] hydrogenases function as ion pumps.

Eha and Ehb hydrogenases contain extra subunits in addition to those shared by other energy-converting [NiFe] hydrogenases (or [NiFe]-hydrogenase-3-type). Eha contains a 6[4Fe-4S] polyferredoxin, a 10[4F-4S] polyferredoxin, ten other predicted integral membrane proteins (EhaA

, EhaB

, EhaC

, EhaD

, EhaE

, EhaF

, EhaG

, EhaI

, EhaK

, EhaL

and

) and four hydrophilic subunits (EhaM, EhaR, EhS, EhT) . The ten predicted integral membrane proteins are absent from Ech, Coo, Hyc and Hyf complexes, which may have simpler membrane components than Eha. Eha and Ehb catalyse the reduction of low-potential redox carriers (e.g. ferredoxins or polyferredoxins), which then might function as electron donors to oxidoreductases.

This entry represents the Energy-converting hydrogenase subunit EhaL from Methanobacteria and Methanococci, including Methanocaldococcus jannaschii.
Protein of unknown function DUF2105, membrane (DUF2105_membrane)
Type: Family

This entry represents a protein found in various hypothetical archaeal proteins, has no known function.
Protein of unknown function DUF2108, membrane (DUF2108_membrane)
Type: Family

This entry is found in various hypothetical archaeal proteins, has no known function.
Protein of unknown function DUF2109, membrane (DUF2109_membrane)
Type: Family

This entry is found in various hypothetical archaeal proteins and has no known function.
Protein of unknown function DUF2115 (DUF2115)
Type: Family

This entry represents various hypothetical archaeal proteins, has no known function.
Protein of unknown function DUF2116, treble clef zinc finger (DUF2116_treble_clef)
Type: Family

This entry contains various hypothetical prokaryotic proteins whose functions are unknown. They contain a conserved treble clef motif in the N-terminal part and a predicted transmembrane segment in the C-terminal part.
Protein of unknown function DUF2118 (DUF2118)
Type: Family

This entry represents a family of hypothetical proteins of unknown function.
Protein of unknown function DUF2119 (DUF2119)
Type: Family

This entry represents a family of hypothetical archaeal proteins of unknown function.
Protein of unknown function DUF2130 (DUF2130)
Type: Family

This entry, found in various hypothetical bacterial proteins, has no known function.
Domain of unknown function DUF2135 (DUF2135)
Type: Domain

This entry, found in various hypothetical prokaryotic proteins, has no known function.
Domain of unknown function DUF2147 (DUF2147)
Type: Domain

This domain is found in various hypothetical prokaryotic proteins, has no known function. It is present in HP1028 (

) from Helicobacter pylori, which may be involved in chemotaxis .
Domain of unknown function DUF2148 (DUF2148)
Type: Domain

This domain, found in various hypothetical bacterial and archaeal proteins containing a ferredoxin domain, has no known function.