SII-SWORD/CoKE huggingface dataset:
Geranylgeranyl transferase type-2 subunit beta (Ptb1)
Type: Family

This entry includes the beta subunit of geranylgeranyl transferase type-2 (GGTase-II), which is also known as Rab geranyl-geranyltransferase subunit beta, Bet2 and Ptb1. GGTase-II catalyses the transfer of a geranyl-geranyl moiety from geranyl-geranyl pyrophosphate to proteins having the C-terminal -XCC or -XCXC . GGTase-IIs are a subgroup of protein prenyltransferases (PTases) of lipid-modifying enzymes. PTases catalyze the carboxyl-terminal lipidation of Ras, Rab, and several other cellular signal transduction proteins, facilitating membrane associations and specific protein-protein interactions. Prenyltransferases employ a Zn2+ ion to alkylate a thiol group catalyzing the formation of thioether linkages between cysteine residues at or near the C terminus of protein acceptors and the C1 atom of isoprenoid lipids (geranylgeranyl (20-carbon) in the case of GGTase-II). GGTase-II catalyzes alkylation of both cysteine residues in Rab proteins containing carboxy-terminal "CC", "CXCX" or "CXC" motifs. PTases are heterodimeric with both alpha and beta subunits required for catalytic activity. The beta subunit has an α6-α6 barrel fold. In contrast to other prenyltransferases, GGTas-II requires an escort protein to bring the substrate protein to the catalytic heterodimer and to escort the geryanylgeranylated product to the membrane .
Phosphohydrolase-associated domain (PHydrolase_assoc_dom)
Type: Domain

This entry represents the phosphohydrolase-associated domain, which is found on bacterial and archaeal deoxyguanosinetriphosphate triphosphohydrolases, which preferentially hydrolyse dGTP over the other canonical NTPs .
Fn3 associated repeat (Fn3_assoc_repeat)
Type: Repeat

The entry represents a Fn3 (fibronectin type III) associated repeat. This repeat is found in several glycosyl hydrolase families of proteins such as a glycoside hydrolase

that may be involved in ulvan degradation or endoglucanase, which is responsible for the endohydrolysis of (1->4)-beta-D-glucosidic linkages in cellulose, lichenin and cereal beta-D-glucans .
DXP reductoisomerase, C-terminal domain (DXPR_C)
Type: Domain

This entry represents the C-terminal domain of the 1-deoxy-D-xylulose-5-phosphate reductoisomerase enzymes. This domain forms a left handed super-helix. DXP reductoisomerase catalyses the NADP-dependent rearrangement and reduction of 1-deoxy-D-xylulose-5-phosphate (DXP) to 2-C-methyl-D-erythritol 4-phosphate (MEP) .
WYL domain (WYL_dom)
Type: Domain

This presumed domain is often found to the C terminus of a DNA-binding helix-turn-helix domain. This domain may be involved in binding to an as yet unknown ligand that allows a transcriptional regulation response to that molecule. There are a number of proteins that contain two tandem copies of this domain such as

. This suggests that this domain may form a dimeric arrangement.
Acetyl-CoA hydrolase/transferase, C-terminal domain (AcetylCoA_hyd_C)
Type: Domain

This entry represents an acetyl-CoA hydrolase/transferase C-terminal domain.
This domain is found in several enzymes which take part in pathways involving acetyl-CoA, including acetyl-CoA hydrolase, succinyl-CoA:coenzyme A transferase (CAT1), propionyl-CoA:succinate CoA transferase, and 4-hydroxybutyrate coenzyme A transferase (CAT2).
Transposase zinc-binding domain (Zn_Tnp)
Type: Domain

This domain is likely to be a zinc-binding domain. It is found at the N terminus of transposases belonging to the IS91 family.
Mononegavirales mRNA-capping domain V (Mononeg_mRNAcap)
Type: Domain

L protein (large polymerase protein) is a polymerase protein. The V domain of L RNA-polymerase carries a new motif, GxxTx(n)HR, that is essential for mRNA cap formation. Nonsegmented negative-sense (NNS) RNA viruses, Mononegavirales, cap their mRNA by an unconventional mechanism. Specifically, 5'-monophosphate mRNA is transferred to GDP derived from GTP through a reaction that involves a covalent intermediate between the large polymerase protein L and mRNA. The V region is essential for this process .
Fibronectin type III-like domain (Fn3-like)
Type: Domain

This domain has a fibronectin type III-like structure . It is often found in association with

and

. Its function is unknown.
Tyrosine/serine-protein phosphatase IphP-type (Tyr/Ser_Pase_IphP-type)
Type: Family

This is a family of putative tyrosine/serine-protein phosphatases. A member of this family, IphP, is a cyanobacterial dual-specificity protein phosphatase with MAP kinase phosphatase activity . This entry also includes PtpB from Mycobacterium tuberculosis. PtpB is a phosphatase that possesses triple substrate specificity toward phosphotyrosine, phosphoserine/threonine and phosphoinositides .
DNAJ-containing protein, X-domain (DnaJ_X)
Type: Domain

In certain plant and yeast proteins, the DnaJ-1 proteins have a three-domain structure. The x-domain lies between the N-terminal DnaJ and the C-terminal Z domains . This domain found in Plasmodium falciparum RESA (ring-infected erythrocyte surface antigen) has been shown to bind to spectrin and stablize the tetramer .
ER membrane protein complex subunit 1 (EMC1)
Type: Family

ER membrane protein complex subunit 1 is a component of the ER membrane protein complex (EMC, composed of EMC1, EMC2, EMC3, EMC4, EMC5 and EMC6). In Saccharomyces cerevisiae, the EMC seems to be required for efficient folding of proteins in the endoplasmic reticulum (ER) .
Transcription termination and cleavage factor, C-terminal domain (CSTF_C)
Type: Domain

The C-terminal section of cleavage stimulation and termination factor CstF-64 (CSTF2) and its yeast orthologue Rna15 form a discreet structure that is crucial for mRNA 3'-end processing . This domain interacts with Pcf11 and possibly PC4, thus linking CSTF2 to transcription, transcriptional termination, and cell growth .

Proteins containing this domain also include Pti1 protein from budding yeast. Pti1 is an essential component of CPF (cleavage and polyadenylation factor) involved in 3' end formation of snoRNA and mRNA .
Intramembrane metalloprotease PrsW (PrsW)
Type: Family

PrsW, appears to be a member of a widespread family of membrane proteins that includes at least one previously known protease. PrsW appears to be responsible for Site-1 cleavage of the RsiW anti-sigma factor, the cognate anti-sigma factor, and it senses antimicrobial peptides that damage the cell membrane and other agents that cause cell envelope stress, the three acidic residues, E75, E76 and E95 in B7GHM8 appear to be crucial since their mutation to alanine renders the protein inactive. Based on predictions of the bioinformatics programme TMHMM it is likely that these residues are located on the extracytoplasmic face of PrsW placing them in a position to act as a sensor for cell envelope stress .
1,3-beta-glucan synthase component FKS1-like, domain-1 (FKS1-like_dom1)
Type: Domain

This domain is likely to be the 'Class I' region just N-terminal to the first set of transmembrane helices that is involved in 1,3-beta-glucan synthesis itself .
RnfC Barrel sandwich hybrid domain (RnfC_N)
Type: Domain

This domain is part of the barrel sandwich hybrid superfamily. It is found at the N-terminal of the RnfC Electron transport complex protein. It appears to be most related to the N-terminal NQRA domain (

).
tRNA uridine 5-carboxymethylaminomethyl modification enzyme MnmG, C-terminal (MnmG_C)
Type: Domain

This entry represents the C-terminal domain of MnmG (also known as GidA). It consists of 4 helices, the last three being rather short and forming small bundle . MnmG is a tRNA modification enzyme found in bacteria and mitochondria that forms a complex with MnmE which is involved in the formation of methyluridine derivatives at the wobble uridine base in some tRNAs . Based on mutational analysis this domain has been suggested to be implicated in binding of the D-stem of tRNA and to be responsible for the interaction with protein MnmE .
Protein ASX-like, PHD domain (ASX-like_PHD)
Type: Domain

This entry represetnts the PHD domain, a DNA-binding domain, on the additional sex combs (ASX) and additional sex combs-like (AsxL) proteins . The Asx protein acts as an enhancer of trithorax and polycomb in displaying bidirectional homoeotic phenotypes in Drosophila, suggesting that it is required for maintenance of both activation and silencing of Hox genes. Asx is required for normal adult haematopoiesis and its function depends on its cellular context .
BspA-type LRR region (LRR_5)
Type: Repeat

This entry represents a leucine rich repeat. A leucine-rich repeat (LRR) is a protein structural motif that forms an α/β horseshoe fold . Leucine-rich repeats are frequently involved in the formation of protein protein interactions .

This repeat is found in a large number of BSPA-like surface antigens from Trichomonas vaginalis.
Cyclin-D1-binding protein 1-like (GCIP-like)
Type: Family

Cyclin-D1-binding protein 1 (CCNDBP1, also known as GCIP) is a helix-loop-helix protein that may negatively regulate cell cycle progression and functions in tumour suppression . It may act, at least in part, via inhibition of the cyclin-D1/CDK4 complex, thereby preventing phosphorylation of RB1 and blocking E2F-dependent transcription . This protein has also been reported to alleviate DNA damage through the activation of the ATM-CHK2 pathway and has been proposed to be used as biomarker to detect certain cancers [

,

}.
Shisa (Shisa)
Type: Family

Shisa is a transmembrane, transcription factor-type protein that physically interacts with immature forms of the Wnt receptor Frizzled and the FGF receptor within the endoplasmic reticulum to inhibit their post-translational maturation and trafficking to the cell surface .

The Shisa family founding member, Xenopus Shisa, promotes head development by antagonising Wnt and FGF signaling . Several vertebrate homologues have been identified with implicated roles in development, cancer and apoptosis . Distantly related Shisa homologues have also been detected that possess an N-terminal domain with six conserved cysteines. These Shisa-like proteins include SHISAL1 (shisa-like-1, also known as KIAA1644), SHISAL2A (FAM159A) and SHISAL2B (FAM159B) from vertebrates .
Adenine deaminase C-terminal domain (Adenine_deam_C)
Type: Domain

This entry represents a C-terminal domain of the adenine deaminase enzyme. Adenine deaminase (

) hydrolyses adenine to form hypoxanthine and ammonia.
Probable methyltransferase-like protein 24 (METTL24)
Type: Family

Methyltransferase-like protein 24 belongs to the methyltransferase superfamily. Its function is not clear.
Adhesion G-protein coupled receptor V1 (ADGRV1)
Type: Family

Adhesion G-protein coupled receptor V1 (ADGRV1), also known as G protein-coupled receptor 98, is a receptor that has an essential role in the development of hearing and vision . It couples to G-alpha(i)-proteins, GNAI1/2/3, G-alpha(q)-proteins, GNAQ, as well as G-alpha(s)-proteins, GNAS, inhibiting adenylate cyclase (AC) activity and cAMP production . Defects in GPR98 are the cause of Usher syndrome type 2C (USH2C). USH is a genetically heterogeneous condition characterised by the association of retinitis pigmentosa with sensorineural deafness . Defects in GPR98 may also be a cause of familial febrile convulsions type 4 (FEB4); also known as familial febrile seizures 4 .
FAX/IsoI-like (FAX/IsoI-like)
Type: Family

This entry includes a group of glutathione S-transferase (GST) domain containing proteins, including FAX (failed axon connections) from animals and uncharacterised proteins from bacteria. Drosophila FAX may play a role in axonal development .
Myelin gene regulatory factor, ICA domain (MYRF_ICA)
Type: Domain

Myelin regulatory factor (Myrf) is a transcription regulator required in vertebrates for expression of central nervous system (CNS) myelin genes such as Mbp and Mog, thereby playing a central role in oligodendrocyte maturation and CNS myelination . It is also required for the maintenance of expression of myelin genes and the mature oligodendrocytes identity in the adult CNS . A Caenorhabditis elegans orthologue, pqn-47, may function as a regulator of molting , while a Dictyostelium orthologue has been described to regulate prestalk differentiation .

This domain is found towards the C terminus of myelin regulatory factor (Myrf) and corresponds to the Intramolecular Chaperone Auto-processing (ICA) domain. It forms a homo-trimer and carries out the auto-cleavage of Myrf releasing the N-terminal homo-trimer from the ER membrane. This allows its entry to the nucleus to function as a homo-trimer transcription factor .
Butirosin biosynthesis protein H, N-terminal (BtrH_N)
Type: Domain

This entry represent the N terminus of the acyl carrier protein:aminoglycoside acyltransferase BtrH. Alternatively it can be referred to as butirosin biosynthesis protein H. BtrH transfers the unique (S)-4-amino-2-hydroxybutyrate (AHBA) side chain, which protects the antibiotic butirosin from several common resistance mechanisms. Butirosin, an aminoglycoside antibiotic produced by Bacillus circulans, exhibits improved antibiotic properties over its parent molecule and retains bactericidal activity toward many aminoglycoside-resistant strains. Butirosin is unique in carrying the AHBA side-chain. BtrH transfers the AHBA from the acyl carrier protein BtrI to the parent aminoglycoside ribostamycin as a gamma-glutamylated dipeptide .
Strawberry notch, helicase C domain (SBNO_Helicase_C_dom)
Type: Domain

Strawberry notch proteins carry DExD/H-box groups and Helicase_C domains. These proteins promote the expression of diverse targets, potentially through interactions with transcriptional activator or repressor complexes .
ZNF706/At2g23090 superfamily (ZNF706/At2g23090_sf)
Type: Homologous_superfamily

Proteins with this domain include zinc finger protein 706 from animals and uncharacterised protein At2g23090 from Arabidopsis.
Ubinuclein middle domain (UBN_middle_dom)
Type: Domain

Ubinuclein 1 and 2 (UBN1, UBN2) are members of a histone chaperone complex involved in the formation of a certain type of facultative heterochromatin, called senescence-associated heterochromatin foci (SAHF) . The domain described here is conserved in many eukaryotes such as human, rat, drosophila, and zebra-fish.
Capsule assembly protein Wzi (Caps_assemb_Wzi)
Type: Family

Many bacteria are covered in a layer of surface-associated polysaccharide called the capsule. These capsules can be divided into four groups depending upon the organisation of genes responsible for capsule assembly, the assembly pathway and regulation . This family plays a role in group 1 capsule biosynthesis. It is likely to be involved in the later stages of capsule assembly.

Structurally, Wzi consists of an 18-stranded β-barrel with a periplasmic helical bundle that has a role in the recognition of the capsular polysaccharide. It is predicted that the Wzi-polysaccharide interaction is critical in the initialisation step of the functional capsule biosynthesis and the later steps of the capsule assembly .
Peptidyl-prolyl cis-trans isomerase like 2, U-box domain (PPIL2_U-box_dom)
Type: Domain

This entry represents the U-box domain found in peptidyl-prolyl cis-trans isomerase like 2 subfamily members. They are peptidyl-prolyl cis-trans isomerases that accelerate the folding of proteins. They catalyse the cis-trans isomerization of proline imidic peptide bonds in oligopeptides .
WVELL protein (WVELL)
Type: Family

This family includes the Bacillus subtilis YfhJ protein

, which is functionally uncharacterised. This is not a homologue of Escherichia coli YfhJ, a synonym for IscX, which belongs to

. This family of proteins is found in bacteria. Proteins in this family are approximately 90 amino acids in length and contain a highly conserved WVELL motif.
PknH-like extracellular domain (PknH-like_Extracell)
Type: Domain

This entry represents the C-terminal extracellular sensor domain of a group of protein kinases found mainly in Mycobacteria, such as PknH . The PknH sensor domain contains six α helices and seven anti-parallel β strands . It is also found in isolation in numerous proteins, for example the lipoproteins lpqQ, lppH and lpqA from Mycobacterium tuberculosis. It contains two completely conserved C residues that are likely to form a disulphide bond. A second pair of cysteines are less well conserved and probably form a second disulphide bond. It seems likely that this domain functions to bind some as yet unknown ligand.
D-serine dehydratase-like domain (D-ser_dehydrat-like_dom)
Type: Domain

This domain is found at the C terminus of yeast D-serine dehydratase, a zinc dependent enzyme . Structures have been solved for two bacterial members of this family.
Reverse transcriptase zinc-binding domain (RVT-Znf)
Type: Domain

This domain would appear to be a zinc-binding region of a putative reverse transcriptase.
PGG domain (PGG_dom)
Type: Domain

The PGG domain is named for the highly conserved sequence motif found at the start of the domain. Its function is not known.
Katanin p80 WD40 repeat-containing subunit B1 (KTNB1)
Type: Family

Katanin is a microtubule-severing protein consist of a 60kDa ATPase subunit (katanin-p60) and a 80kDa subunit (katanin-p80) ,

]. Katanin-p80 is composed of an N-terminal WD40 repeat domain, a central proline-rich domain and a C-terminal domain required for dimerisation with the catalytic katanin-p60 . The katanin complex associates with a specific subregion of the mitotic spindle leading to increased microtubule disassembly and targeting of katanin-p60 to the spindle poles . Katanin is a crucial regulator of early embryonic development, and recessive mutations or deletions in the KATNB1 gene cause severe microcephaly or microlissencephaly . Katanin forms a complex with another microcephaly-associated protein, ASPM (abnormal spindle-like microcephaly-associated) that controls spindle pole organization, poleward spindle flux, and spindle positioning, processes that when misregulated could perturb proliferation of neuronal progenitors and lead to microcephaly. Katanin also interacts with CAMSAPs (calmodulin-regulated spectrin-associated proteins) and is required for limiting the length of CAMSAP-bound MT minus-end stretches during interphase . In plants it also plays an important role as it is required for the bending of the plant axis toward the light source.
Neurofascin, immunoglobulin-like domain (NFASC_Ig-like)
Type: Domain

Neurofascin (NFASC) is a cell adhesion, ankyrin-binding protein which may be involved in neurite extension, axonal guidance, synaptogenesis, myelination and neuron-glial cell interactions . This protein belongs to the L1 subfamily of cell adhesion molecules (CAMs) and is comprised of an extracellular region having six Ig-like domains and five fibronectin type III domains, a transmembrane region, and a cytoplasmic domain. NFASC has many alternatively spliced isoforms having different temporal expression patterns during development. NF participates in axon subcellular targeting and synapse formation, however little is known of the functions of the different isoforms.

This entry represents the first immunoglobulin-like (Ig-like) domain.
Neurofascin/L1/NrCAM, C-terminal domain (Neurofascin/L1/NrCAM_C)
Type: Domain

This is the very C-terminal region of nervous system cell adhesion molecules neuroglian, neurofascin, neural adhesion molecule L1, NrCAM and NgCAM . It lies upstream of the IG and Fn3 domains and has the highly conserved motif FIGEY. The function is not known.
3-oxoadipate enol-lactonase 1/2 (PcaD/CatD)
Type: Family

This entry includes 3-oxoadipate enol-lactonase 1 and 2. These proteins are 3-oxoadipate enol-lactonases (also called beta-ketoadipate enol-lactone hydrolase), which catalyse the fourth step in the protocatechuate degradation to beta-ketoadipate and then to succinyl-CoA and acetyl-CoA .
Condensin subunit 1/Condensin-2 complex subunit D3 (CND1/NCAPD3)
Type: Family

This entry includes condensin subunit 1 (CND1) and condensin-2 complex subunit D3 (NCAPD3).

CND1 is a regulatory subunit of the condensin complex (contains the SMC2 and SMC4 heterodimer, and three non SMC subunits that probably regulate the complex: NCAPH/BRRN1, NCAPD2/CAPD2 and NCAPG), a complex required for conversion of interphase chromatin into mitotic-like condense chromosomes . The condensin complex probably introduces positive supercoils into relaxed DNA in the presence of type I topoisomerases and converts nicked DNA into positive knotted forms in the presence of type II topoisomerases .
Dynein heavy chain (DHC)
Type: Family

Dyneins are described as motor proteins of eukaryotic cells, as they can convert energy derived from the hydrolysis of ATP to force and move along cytoskeletal polymers, such as microtubules. Dyneins generally contain one to three heavy chains, where each heavy chain consists of a C-terminal globular head, a flexible microtubule-binding stalk, and a flexible N-terminal tail known as the cargo-binding domain . The two categories of dyneins are the axonemal dyneins, which produce the bending motions that propagate along cilia and flagella, and the cytosolic dyneins, which drive a variety of fundamental cellular processes including nuclear migration, organisation of the mitotic spindle, chromosome separation during mitosis, and the positioning and function of many intracellular organelles. Cytoplasmic dyneins contain several accessory subunits ranging from light to intermediate chains.
Fanconi anemia-associated protein of 24kDa (FAAP24)
Type: Family

Fanconi anemia-associated protein of 24kDa (FAAP24) plays a role in DNA repair through recruitment of the FA core complex to damaged DNA. It regulates FANCD2 monoubiquitination upon DNA damage. When repressed, it induces chromosomal instability as well as hypersensitivity to DNA cross-linking agents. It targets FANCM/FAAP24 complex to the DNA, preferentially to single strand DNA .

Fanconi anemia (FA) is a human disorder characterised by cancer susceptibility and cellular sensitivity to DNA crosslinks and other damages. The FA complex repairs the interstrand cross-linking (ICL) lesions and coordinates activities of the downstream DNA repair pathway including nucleotide excision repair, translesion synthesis, and homologous recombination. It is required for the monoubiquitylation of FANCD2 and FANCI heterodimer. The FA core complex consists of FANCA, FANCB, FANCC, FANCE, FANCF, FANCG, FANCL, FANCM, FANCT (UBET2), FAAP100 and FAAP24 .
WD repeat-containing protein 18, C-terminal domain (Wdr18_C_dom)
Type: Domain

WD repeats are short subdomains of about 40 amino acids and fold into 4 anti-parallel β hairpins. The domain represented by this entry has been detected on the C terminus of WD repeat-containing protein 18 (Wdr18), which palys a role during development .
YaaC-like protein (YaaC-like)
Type: Family

The YaaC-like protein family includes the Bacillus subtilis YaaC protein

, which is functionally uncharacterised. This family of proteins is found in bacteria.
Transposon-encoded protein TnpV (TnpV)
Type: Family

This family of proteins is functionally uncharacterised. It is found in bacteria and viruses.
Transposon-encoded protein TnpW (TnpW)
Type: Family

This family of proteins is found in bacteria. There is a single completely conserved residue G that may be functionally important.
Non-haem dioxygenase, N-terminal domain (DIOX_N)
Type: Domain

This is the highly conserved N-terminal region of proteins with 2-oxoglutarate/Fe(II)-dependent dioxygenase activity . It is also found in Isopenicillin N synthase , 1-aminocyclopropane-1-carboxylate oxidase , Gibberellin oxidases and dioxygenases and other related proteins.