SII-SWORD/CoKE huggingface dataset:
PCIF1, WW domain (PCIF1_WW)
Type: Domain

This domain is found in bacteria and eukaryotes, and is approximately 180 amino acids in length. It is the WW domain of PCIF1. PCIF1 interacts with phosphorylated RNA polymerase II carboxy-terminal domain (CTD). The WW domain of PCIF1 can directly and preferentially bind to the phosphorylated CTD compared to the unphosphorylated CTD. PCIF1 binds to the hyperphosphorylated RNAP II (RNAP IIO) in vitro and in vivo. Double immunofluorescence labeling in HeLa cells demonstrated that PCIF1 and endogenous RNAP IIO are co-localized in the cell nucleus. PCIF1 is a cap-specific adenosine methyltransferase that catalyzes formation of N6,2'-O-dimethyladenosine cap (m6A(m)) by methylating the adenosine at the second transcribed position of capped mRNAs .
Protein of unknown function DUF3605 (DUF3605)
Type: Family

This family of proteins is found mostly in fungi, including N-acetylglucosamine-induced protein 1 (Gig1) from Candida albicans. Gig1 plays a role in the N-acetylglucosamine metabolic pathway .
Protein of unknown function DUF3606 (DUF3606)
Type: Family

This family of proteins is found in bacteria. Proteins in this family are typically between 58 and 85 amino acids in length. There is a single completely conserved residue G that may be functionally important.
Ig-like domain, bacterial type (Ig-like_bact)
Type: Domain

This entry represents a domain with an Ig-like fold, found in a variety of bacterial surface proteins.
Post-transcriptional regulator MKT1, C-terminal (MKT1_C)
Type: Domain

Mkt1 interacts with the Poly(A)-binding protein associated factor, Pbp1, and is present at the 3' end of RNA transcripts during translation. The Mkt1-Pbp1 complex is involved in the post-transcriptional regulation of HO endonuclease expression . In trypanosome, zinc finger protein ZC3H11 interacts with MKT1 and PBP1 through it's C-terminal region, those interactions are essential for survival of the mammalian-infective bloodstream form .

This entry represents a domain is found in the C-terminal region of MKT1.
Post-transcriptional regulator MKT1, N-terminal (MKT1_N)
Type: Domain

Mkt1 interacts with the Poly(A)-binding protein associated factor, Pbp1, and is present at the 3' end of RNA transcripts during translation. The Mkt1-Pbp1 complex is involved in the post-transcriptional regulation of HO endonuclease expression . In trypanosome, zinc finger protein ZC3H11 interacts with MKT1 and PBP1 through it's C-terminal region, those interactions are essential for survival of the mammalian-infective bloodstream form .

This entry represents a domain is found in the N-terminal region of MKT1.
Farnesoic acid O-methyl transferase (Methyltransf_FA)
Type: Domain

This domain, found in farnesoic acid O-methyl transferase, is approximately 110 amino acids in length. Farnesoic acid O-methyl transferase (FAMeT) is the enzyme that catalyses the formation of methyl farnesoate (MF) from farnesoic acid (FA) in the biosynthetic pathway of juvenile hormone (JH) .
snRNA-activating protein complex, subunit 3 (snRNA-activating_su3)
Type: Family

snRNA-activating protein complex 50kDa subunit (SNAP50), also known as subunit 3, is part of the snRNA-activating protein complex which activates RNA polymerases II and III . It contains a cysteine-histidine cluster with two possible zinc finger motifs.
Chromatin assembly factor 1 subunit A, dimerization domain (CAF1A_DD)
Type: Domain

The CAF-1 or chromatin assembly factor-1 consists of three subunits, p150, p60 and p48 and this entry includes the largest, p150 or A . Subunit p150 is uniquely required for the progression of S phase in mouse cells , independent of its ability to promote histone deposition but dependent on its ability to interact with HP1 - heterochromatin protein 1-rich heterochromatin domains next to centromeres that are crucial for chromosome segregation during mitosis. It contains a HP1-CAF-1 interaction module that functions as a built-in replication control for heterochromatin, which, like a control barrier, has an impact on S-phase progression in addition to DNA-based checkpoints . p150 plays a key role in embryonic development .

This entry represents the dimerization domain of p150 .
Insecticide toxin TcdB middle/C-terminal (TcdB_toxin_mid/C)
Type: Domain

This domain family is found in bacteria, and is approximately 150 amino acids in length. It occurs in the C-terminal-sided middle region of the bacterial insecticide toxin TcdB.
Insecticide toxin TcdB middle/N-terminal (TcdB_toxin_mid/N)
Type: Domain

This domain family is found in bacteria and archaea, and is typically between 164 and 180 amino acids in length. The family is found in association with

. This domain is the N-terminal-sided middle region of the bacterial insecticide toxin TcdB.
Microcephalin-like (Microcephalin-like)
Type: Family

Microcephalin is implicated in chromosome condensation and DNA damage induced cellular responses . It may play a role in neurogenesis and regulation of the size of the cerebral cortex in animals. It is a protein, which if expressed homozygously, causes the organism to have the condition microcephaly - a drastically reduced brain mass and volume . Microcephalin is predicted to contain three BRCA1 C-terminal domains, the first of which is the probable microcephaly mutation site.

This entry includes non-mammalian uncharacterised proteins (from lower vertebrates and fungi) related to microcephalin.
Envelope fusion protein-like (Envelope_fusion-like)
Type: Family

This entry includes the Baculovirus envelope fusion protein, which is an envelope glycoprotein mediating the fusion of viral and host endosomal membranes leading to virus entry into the host cell . Protein AC23, which is a nonfunctional F-like protein from the Autographa californica nuclear polyhedrosis virus, is a pathogenicity factor that accelerates mortality in the host insect .

This entry also includes transposable element that have sequence similarity to the envelope fusion proteins of Baculovirus, such as retrovirus-related Env polyprotein from copia-like transposable element 17.6 (Env 17.6) from Drosophila melanogaster .
FAM69, protein-kinase domain (FAM69_kinase_dom)
Type: Domain

This is the C-terminal region of a family of FAM69 proteins from Metazoa and Viridiplantae that are active protein-kinases. The family members have a short transmembrane helix close to the N terminus, and thereafter are highly enriched with cysteines. FAM69 proteins are localised to the endoplasmic reticulum. Many members also have a short EF-hand, calcium-binding, domain just upstream of the kinase domain. The exact function of the more N-terminal family is uncertain.
Thermostable hemolysin (T_hemolysin)
Type: Family

This family of proteins is found in bacteria. Thermostable haemolysin is a pore-forming toxin of bacteria, able to lyse erythrocytes from a number of mammalian species .
Protein of unknown function DUF3611 (DUF3611)
Type: Family

This entry represents a group of proteins mostly from plants and Cyanobacteria (blue-green algae), including TIC21 from Arabidopsis. TIC21 is Involved in chloroplast protein import across the inner envelope membrane. It can acts as a chloroplast permease regulating the iron transport and homeostasis .
Histone-binding protein RBBP4-like, N-terminal (Histone-bd_RBBP4-like_N)
Type: Domain

This entry rerpesnts the N-terminal domain of the histone-binding protein RBBP4. Proteins containing this domain include members from the WD repeat RBAP46 (RBBP7)/RBAP48(RBBP4)/MSI1 family.

RBBP4 is a subunit of the chromatin assembly factor 1 (CAF-1) complex. The CAF-1 complex is a conserved heterotrimeric protein complex that promotes histone H3 and H4 deposition onto newly synthesized DNA during replication or DNA repair; specifically it facilitates replication-dependent nucleosome assembly with the major histone H3 (H3.1). This domain is an α helix which sits just upstream of the WD40 seven-bladed β-propeller in the human RBBP7 protein. RBBP7 folds into the β-propeller and binds histone H4 in a groove formed between this N-terminal helix and an extended loop inserted into blade six .
Protein of unknown function DUF3613 (DUF3613)
Type: Family

This family of proteins is found in bacteria. Proteins in this family are typically between 94 and 126 amino acids in length.
Protein of unknown function DUF3614 (DUF3614)
Type: Family

This family of proteins is found in viruses. Proteins in this family are typically between 162 and 495 amino acids in length.
Protein of unknown function DUF3612 (DUF3612)
Type: Family

This domain family is found in bacteria, and is approximately 180 amino acids in length. The family is found in association with

.
CpG binding protein, C-terminal (CpG-bd_C)
Type: Domain

CpG-binding protein is a transcriptional activator that exhibits a DNA binding specificity for unmethylated CpG motifs . CpG is made of a PHD1, an acidic, a basic, a coiled-coil, and a PHD2 domains . This protein contains three cysteine-rich domains identified at the N-terminal, central region, and C-terminal of the protein, where the central cysteine-rich domain is located within the DNA-binding domain, found between PHD1 and the acidic domains .

This domain is found in eukaryotes, and is approximately 240 amino acids in length. It is found at the C-terminal of the CpG-binding protein containing the coiled-coil and PHD2 domains.
Chitin synthase export chaperone (Chs7)
Type: Family

Chs7 is an integral membrane protein that acts as a chaperone for the export of the chitin synthase Chs3 from the endoplasmic reticulum .
Domain of unknown function DUF3615 (DUF3615)
Type: Domain

This domain is found in a group of uncharacterised plant proteins, and is typically between 86 and 97 amino acids in length. There is a conserved FAE sequence motif. There is a single completely conserved residue F that may be functionally important.
Domain of unknown function DUF3616 (DUF3616)
Type: Domain

This entry represents a domain found in a group of bacterial proteins. There is a conserved GLRGPV sequence motif.
Protein of unknown function DUF3617 (DUF3617)
Type: Family

This family of proteins is found in bacteria. Proteins in this family are typically between 155 and 179 amino acids in length. There is a single completely conserved residue C that may be functionally important.
Protein of unknown function DUF3618 (DUF3618)
Type: Family

This domain family is found in bacteria, and is approximately 50 amino acids in length.
Complementary sex determination, N-terminal (Sex_determin_N)
Type: Domain

This entry represents the N-terminal end of the sex determination protein.

Sex determination proteins are found in eukaryotes. Proteins in this family are typically between 168 and 410 amino acids in length. It plays a role in the gender determination of around 20% of all animals.

In the honeybee, the mechanism of sex determination depends on the complementary sex determiner (csd) gene which produces an SR-type protein. Males are hemizygous (haploid) or homozygous for csd alleles while females are heterozygous (diploid). Heterozygosity generates an active protein which initiates female development .

When the csd gene is heterozygous, it activates the feminizer gene (fem) by directing the splicing to form female fem mRNAs, which encode the Fem protein . This leads to female development. In contrast, hemizygous or homozygous csd genes are non-active, resulting in male-specific splicing of fem mRNAs .
Protein of unknown function DUF3619 (DUF3619)
Type: Family

This protein is found in bacteria. Proteins in this family are about 140 amino acids in length. This protein has two conserved sequence motifs: AAR and DDLP.
Uncharacterised protein family, TMEM59 (Uncharacterised_TMEM59)
Type: Family

This family of proteins is found in eukaryotes. Proteins in this family are typically between 285 and 331 amino acids in length. BSMAP has a putative transmembrane domain and is predicted to be a type I membrane glycoprotein.
Histidine kinase PdtaS, GAF domain (PdtaS_GAF)
Type: Domain

This entry represents the GAF domain of the sensor region in the cytosolic histidine kinase (HK), PdtaS, from Mycobacterium tuberculosis. The N-terminal region of this protein is comprised of closely linked GAF and PAS domains, both are ubiquitous and form dimeric interfaces. GAF domains are known to bind heme (as can PAS domains), to be involved in redox responses and even to function as catalytic domains .

PdtaS is a member of the two-component regulatory system PdtaR/PdtaS , which plays an essential role in mycobacterial adaptation to poor nutrient conditions. Under nutrient deprivation, there is an increase of intracellular concentrations of c-di-GMP which binds to the PdtaS sensor and promotes its autophosphorylation, leading to the activation of the signaling cascade .
Homeobox protein Hox1A3 N-terminal (HoxA13_N)
Type: Domain

This domain represents the N-terminal region of HoxA13 and other Hox proteins (HoxB13, HoxC13 and HoxD13). HoxA13 is involved in formation of the digital arch of the hands and feet, as well as in correct genital formation . This domain is found in association with

.
Mamastrovirus p20 protein (Mamastrovirus_p20)
Type: Family

This family of proteins is found in mamastroviruses such as human astrovirus. This entry represents the p20 protein .
Protein of unknown function DUF3622 (DUF3622)
Type: Family

This family of proteins is found in bacteria. Proteins in this family are typically between 72 and 107 amino acids in length. There is a conserved VSK sequence motif.
Cytoplasmic activation/proliferation-associated protein-1 C term (Caprin-1_C)
Type: Domain

This family of proteins is found in eukaryotes. Proteins in this family are typically between 343 and 708 amino acids in length. This family is the C-terminal region of caprin-1. Caprin-1 is a protein involved in regulating cellular proliferation. In mutated phenotypes, the G1 phase of the cell cycle is greatly lengthened, impairing normal proliferation. The C-terminal region of caprin-1 contains RGG motifs which are characteristic of RNA binding domains. It is possible that caprin-1 functions through an RNA binding mechanism.
Rotavirus VP1 RNA-directed RNA polymerase, C-terminal (Rotavirus_VP1_C)
Type: Domain

This domain is the C-terminal bracelet domain of the rotavirus protein VP1, an RNA-directed RNA polymerase. It surrounds the exit tunnel for dsRNA produced by replication and for the RNA template for transcription .
Protein of unknown function DUF3624 (DUF3624)
Type: Family

This family of proteins is found in bacteria. Proteins in this family are approximately 90 amino acids in length. There is a conserved GRC sequence motif.
Putative outer membrane core complex of type IVb secretion (T4BSS_DotH_IcmK)
Type: Family

This is a family of bacterial transporter proteins from Proteobacteria. DotH is an integral outer membrane component and it may form an outer membrane complex along with DotD and DotC functionally equivalent to secretins. DotH is the strongest candidate for the VirB9 counterpart of other T4BSS systems .
Protein of unknown function DUF3626 (DUF3626)
Type: Family

This family of proteins is found in bacteria. Proteins in this family are typically between 294 and 374 amino acids in length.
Symplekin C-terminal (Symplekin_C)
Type: Domain

This domain is found in symplekin. It is approximately 180 amino acids in length and contains a single completely conserved residue P that may be functionally important.
Limbin (Limbin)
Type: Family

Limbin (EVC2) interacts with AVC and is a positive regulator of the hedgehog signaling pathway. It plays a critical role in bone formation and skeletal development and may be involved in early embryonic morphogenesis .
ATP-dependent RNA helicase RhlB (RhlB)
Type: Family

Proteins in this entry are DEAD Box RhlB RNA Helicases found in Xanthomonadaceae bacteria.
CD99 antigen-like protein 2 (CD99L2)
Type: Family

This family of proteins is found in eukaryotes. Proteins in this family are typically between 165 and 237 amino acids in length. CD99L2 and CD99 are involved in trans-endothelial migration of neutrophils in vitro and in the recruitment of neutrophils into inflamed peritoneum.
Protein of unknown function DUF3629 (DUF3629)
Type: Family

This family of proteins is found in eukaryotes. Proteins in this family are typically between 256 and 292 amino acids in length.
Protein of unknown function DUF3630 (DUF3630)
Type: Family

This family of proteins is found in bacteria. Proteins in this family are approximately 100 amino acids in length. There is a single completely conserved residue D that may be functionally important.
Domain of unknown function DUF3631 (DUF3631)
Type: Domain

This domain is found in uncharacterised proteins and in tripartite motif containing (TRIM) protein 41. This protein functions as an E3 ligase that catalyzes the ubiquitin-mediated degradation of protein kinase C .
Noelin domain (Noelin_dom)
Type: Domain

This domain is found in eukaryotes, and is approximately 100 amino acids in length. The family is found in association with

. There are two conserved sequence motifs: SAQ and VQN. It is found in Noelin, a glycoprotein which is secreted mainly by postmitotic neurogenic tissues in the developing central and peripheral nervous systems, first appearing after neural tube closure .
KIF-1 binding protein (KBP)
Type: Family

KIF1 binding protein (KBP) is a binding partner for KIF1Balpha that is a regulator of its transport function and thus represents a type of kinesin interacting protein .
Transcription factor Elf, N-terminal (TF_Elf_N)
Type: Domain

Elf (E74-like-factor) is a subfamily of the ETS transcription factor family . Elf-1 is an immune cell specific transcription factor. It is found in T cells, B cells, megakaryocytes,and mast cells and is involved in the control of transcription for various immune proteins . Included in the Elf subfamily are also Elf-2 (NERF) and Elf4 (MEF) .

This entry represents a domain found in the N terminus of Elf transcription factors. It is approximately 110 amino acids in length and is found in association with

. It contains a conserved PAVIVE sequence motif.
Oxopyrrolidines biosynthesis cluster protein G (OpdG)
Type: Family

This family includes oxopyrrolidines biosynthesis cluster protein G (OpdG) which is part of the gene cluster that mediates the biosynthesis of oxopyrrolidines, polyketide-amino acid hybrid compounds with feature structures of tetramic acid .
Inner membrane complex protein (IMCp)
Type: Family

This domain is found in bacteria and eukaryotes. This domain is about 120 amino acids in length. This family is the inner membrane complex of parasitic organisms. This is a cytoskeletal structure associated with the pellicle of these parasites.
Protein DA1-like domain (DA1-like_dom)
Type: Domain

Proteins containing this domain include protein DA1 and its homologues.

In Arabidopsis thaliana, DA1 is a ubiquitin-activated endopeptidase that limits final seed and organ size by restricting the period of cell proliferation . DA1 is activated by the RING E3 ligases Big Brother and DA2, both of which are then inactivated by cleavage by the active peptidase. DA1 also cleaves and inactivates deubiquitinase UBP15 and transcription factors TCP15 and TCP22, all of which promote cell proliferation. Presence of an HEXXH motif, which when mutated leads to inactivity, suggests that DA1 is a metalloendopeptidase .
Intraflagellar transport complex B protein 46 (Intraflagellar_transp_cmplxB)
Type: Family

This family of proteins is found in eukaryotes. Proteins in this family are typically between 298 and 416 amino acids in length. IFT46 is a flagellar protein of complex B. Like all IFT (Intraflagellar transport) proteins, it is required for transport of IFT particles into the flagella .
Tryptophan/threonine-rich plasmodium antigen, C-terminal (Plasmodium-antigen_C)
Type: Domain

This domain is found in the C-terminal region of the surface antigen of malarial Plasmodium species. This antigen is currently being targeted for use as part of a subunit vaccine against Plasmodium falciparum, the main species involved in causing human malaria .
Protein of unknown function DUF3634 (DUF3634)
Type: Family

This family of proteins is found in bacteria. Proteins in this family are typically between 103 and 114 amino acids in length.
TATA element modulatory factor 1, TATA binding (TMF_TATA-bd)
Type: Domain

This is the C-terminal conserved coiled coil region of a family of TATA element modulatory factor 1 proteins conserved in eukaryotes . The proteins bind to the TATA element of some RNA polymerase II promoters and repress their activity. by competing with the binding of TATA binding protein. TMF1_TATA_bd is the most conserved part of the TMFs . TMFs are evolutionarily conserved golgins that bind Rab6, a ubiquitous ras-like GTP-binding Golgi protein, and contribute to Golgi organisation in animal and plant cells. The Rab6-binding domain appears to be the same region as this C-terminal family .
TATA element modulatory factor 1 DNA binding (TMF_DNA-bd)
Type: Family

This is the middle region of a family of TATA element modulatory factor 1 (TMF1) proteins conserved in eukaryotes that contains at its N-terminal section a number of leucine zippers that could potentially form coiled coil structures. The whole proteins bind to the TATA element of some RNA polymerase II promoters and repress their activity by competing with the binding of TATA binding protein. TMFs are evolutionarily conserved golgins that bind Rab6, a ubiquitous ras-like GTP-binding Golgi protein, and contribute to Golgi organisation in animal and plant cells.
Rad26-like, helical repeats (Rad26-like_helical)
Type: Domain

This domain is found in fungal proteins, including Rad26 (

) from Myceliophthora thermophila, a functional subunit of the Rad3-Rad26 complex that is responsible for bringing the kinase to sites of DNA damage. The central region of Rad26 is formed by five helical repeats forming an α-solenoid arrangement .
Outer membrane protein B, passenger domain, Rickettsia (OmpB_passenger_Rickettsia)
Type: Domain

This domain is found in the outer membrane protein B of Rickettsia (rOmpB), a surface-exposed major structural protein which is involved in adhesion and invasion of host cells, playing a role as a rickettsial virulence factor and immunogen during infection, as it serves as a protective envelope . These proteins contain two structural segments, an N-terminal long passenger domain (composed of a β-solenoid structural repeat), that serves as an adhesin and a C-terminal β-barrel, an autotransporter domain

. The passenger domain is methylated at its lysine residues by PKMT1 and PKMT2, and this methylation appears to be associated with rickettsial pathogenicity and immunogenic response . This entry covers a section found in the middle region of the passenger domain.
SBF1/SBF2 domain (SBF1/SBF2)
Type: Domain

This domain is found in eukaryotes, and is approximately 220 amino acids in length. It is found in association with

,

. It is found is the middle region of SBF1 and SBF2, members of the myotubularin family. Myotubularin-related proteins have been suggested to work in phosphoinositide-mediated signalling events that may also convey control of myelination. Mutations of SBF2 are implicated in Charcot-Marie-Tooth disease . SBF2 is a guanine nucleotide exchange factor (GEF) which activates RAB21 and possibly RAB28 .
Transcription factor SOX (SOX_fam)
Type: Family

This entry represents a group of eukaryotic transcription factors known as SOX . Proteins in this family usually contain the high mobility group box domain (

). They are regulators of cell fate decisions during development .
Protein of unknown function DUF3637 (DUF3637)
Type: Family

This domain family is found in viruses, and is approximately 70 amino acids in length. The family is found in association with

,

.
Domain of unknown function DUF3638 (DUF3638)
Type: Domain

This domain is found in eukaryotes, and is approximately 230 amino acids in length. There are two conserved sequence motifs: LLE and NMG.