SII-SWORD/CoKE huggingface dataset:
Mediator of RNA polymerase II transcription subunit 14, RM3 (RM3_Med14)
Type: Domain

This entry represents a domain found in the human Mediator of RNA polymerase II transcription subunit 14 (Med14) and related animal proteins. This entry represents repeat RM3.

Med14 is a component of the Mediator complex, a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. Mediator is recruited to promoters by direct interactions with regulatory proteins and serves as a scaffold for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors . Med14 along with Med17 are scaffold subunits in nucleating Mediator . The major portion of Med14 exists in the Head-Shoulder module of the Mediator and consists of nine tandem repeats (RM1 to RM9), which are arranged in an atypical right-handed helix .
MEIOB-like, N-terminal (OB_MEIOB_N)
Type: Domain

This domain is found at the N-terminal end of human Meiosis-specific with OB domain-containing protein (MEIOB). This domain is predicted to adopt an OB fold.

This domain is also found in Protein hold'em which is the MEIOB homologue in Drosophila. Mutations in this protein result in reduced meiotic crossover formation and sensitivity to the DNA-damaging agent methyl methanesulfonate .

MEIOB is a single-stranded DNA-binding protein required for homologous recombination in meiosis I . It is required for double strand breaks repair and crossover formation and promotion of faithful and complete synapsis. MEIOB binds to single-stranded DNA and exhibits 3'-5' exonuclease activity. MEIOB forms a complex with RPA and with SPATA22, and these three proteins co-localize in foci that are associated with meiotic chromosomes .
Meiotically up-regulated gene 62 protein-like, alpha-beta domain (Mug62_dom)
Type: Domain

This domain is found in Meiotically up-regulated gene 62 protein from Schizosaccharomyces pombe (Mug62) and similar proteins predominantly found in fungi, including Homeostatic regulator of DAG . Mug62 plays a role in meiosis. This domain is often found associated to

and

.
MOM1, alpha-helical domain (MOM1_dom)
Type: Domain

This domain is found in Helicase protein MOM1 from Arabidopsis thaliana (MOM1) and similar plant proteins. MOM1 is involved in the regulation of transcriptional gene silencing (TGS) independently of changes in DNA methylation . This domain is predicted to have an all-α helical configuration.
Nephrocystin 3, helical domain (NPHP3_hel)
Type: Domain

This entry represents a mostly helical domain found in nephrocystin-3 (NPHP3) and related proteins from animals.

NPHP3 is a protein required for normal ciliary development and function. It inhibits disheveled-1-induced canonical Wnt-signalling activity and may also play a role in the control of non-canonical Wnt signalling which regulates planar cell polarity . Loss of the NPHP3 function results in situs inversus, congenital heart defects, and embryonic lethality in mice .
Nephrocystin 3-like, N-terminal (NPHP3-like_N)
Type: Domain

This entry represents a P-loop like domain found at the N-terminal of nephrocystin-3 (NPHP3) as well as in the Ankyrin repeat domain-containing protein 50, Ankyrin repeat domain-containing protein SAT10, Vegetative incompatibility protein HET-E-1 and other related eukaryotic and bacterial proteins.

This domain belongs to NACHT NTPases clade defined by a residue (glycine, alanine or serine) directly C-terminal of the Mg2+-coordinating aspartate, and two additional acidic residues one position downstream, with a consensus sequence hhhhD[GAS]hDE .

NPHP3 is a protein required for normal ciliary development and function. It inhibits disheveled-1-induced canonical Wnt-signalling activity and may also play a role in the control of non-canonical Wnt signalling which regulates planar cell polarity . Loss of the NPHP3 function results in situs inversus, congenital heart defects, and embryonic lethality in mice .

Ankyrin repeat domain-containing protein 50 is involved in the endosome-to-plasma membrane trafficking and recycling of SNX27-retromer-dependent cargo proteins, such as GLUT1 .

Ankyrin repeat domain-containing protein SAT10 is part of the satratoxin SC1 cluster involved in the biosynthesis of satratoxins, trichothecene mycotoxins that are associated with human food poisonings .
Nephrocystin-3, TPR-repeats region (TPR_NPHP3)
Type: Domain

This entry represents a tetratricopeptide repeats (TPR) region found at the nephrocystin-3 (NPHP3) and related proteins from animals.

NPHP3 is a protein required for normal ciliary development and function. It inhibits disheveled-1-induced canonical Wnt-signalling activity and may also play a role in the control of non-canonical Wnt signalling which regulates planar cell polarity . Loss of the NPHP3 function results in situs inversus, congenital heart defects, and embryonic lethality in mice .
Nephrocystin-3, alpha-beta domain (NPHP3_ab_dom)
Type: Domain

This domain is found in human Nephrocystin-3 (NPHP3) and similar animal proteins. This domain is predicted to show a β-sheet with α-helices at both sides.

NPHP3 is a protein required for normal ciliary development and function. It inhibits disheveled-1-induced canonical Wnt-signalling activity and may also play a role in the control of non-canonical Wnt signalling which regulates planar cell polarity . Loss of the NPHP3 function results in situs inversus, congenital heart defects, and embryonic lethality in mice .
Nesprin-1/2 domain (SYNE1/2_dom)
Type: Domain

This domain is found in human Nesprin-1/2 (SYNE1, SYNE2) and similar sequences from vertebrates. It is found towards the C-terminal end of the protein between spectrin repeats (

). Its specific function is unknown.

SYNE1 is a a multi-isomeric modular protein which forms a linking network between organelles and the actin cytoskeleton to maintain the subcellular spatial organisation. This protein has been associated with several severe disorders. SYNE1 and SYNE2 mediate centrosome migration and are both essential for ciliogenesis . SYNE2 assemble with SUN2 in arrays of transmembrane actin-associated nuclear (TAN) lines which are bound to F-actin cables and couple the nucleus to retrograde actin flow during actin-dependent nuclear movement .
NET2A-D/KIP1-like, alpha-helical domain (NET2A-D/KIP1-like_dom)
Type: Domain

This entry represents a domain found in Protein NETWORKED 2A/B/C/D from Arabidopsis thaliana (NET2A/B/C/D), Kinase-interacting protein 1 (KIP1) from Petunia integrifolia and similar plant proteins. This domain is predicted to adopt an all-α configuration.

Plant-specific Networked 2 (NET2) family of actin-binding proteins localise to the actin cytoskeleton and specify different membrane compartments . NET2A, the founding member of this family, associates with F-actin at the plasma membrane in growing pollen tubes . This protein is anchored at the plasma membrane and predominates at cell junctions, the plasmodesmata, and is probably involved in mediating actin-membrane interactions . KIP1, another member of the NET2 family, interacts very strongly with PRK1-K , a receptor-like kinase of petunia, and is probably involved in the receptor-like kinase-mediated signal transduction pathway .
NET2A-D/KIP1-like, C-terminal domain (NET2A-D/KIP1-like_C)
Type: Domain

This domain is found at the C-terminal end of Protein NETWORKED 2A/B/C/D from Arabidopsis thaliana (NET2A/B/C/D), Kinase-interacting protein 1 (KIP1) from Petunia integrifolia and similar plant proteins. This domain is predicted to have an all-α helical configuration.

Plant-specific Networked 2 (NET2) family of actin-binding proteins localise to the actin cytoskeleton and specify different membrane compartments . NET2A, the founding member of this family, associates with F-actin at the plasma membrane in growing pollen tubes . This protein is anchored at the plasma membrane and predominates at cell junctions, the plasmodesmata, and is probably involved in mediating actin-membrane interactions . KIP1, another member of the NET2 family, interacts very strongly with PRK1-K , a receptor-like kinase of petunia, and is probably involved in the receptor-like kinase-mediated signal transduction pathway .
ATP-dependent RNA helicase DHX29-like, UBA domain (UBA_DHX29-like)
Type: Domain

This predicted UBA domain is found at the N-terminal of human ATP-dependent RNA helicase DHX29, which is involved in translation initiation. This domain is also found in DExH-box ATP-dependent RNA helicase DExH4 and 7 from Arabidopsis.

ATP-dependent RNA helicase DHX29 is a DExH-box protein involved in eukaryotic translation initiation. Eukaryotic translation initiation begins with assembly of a 43S preinitiation complex which then attaches to the mRNA and starts scanning the 5'-UTR to the initiation codon. DHX29 is required to bind to the 40S subunit of the 43S preinitiation complex to allow highly structured 5'-UTRs to be scanned. DHX29 has been shown to hydrolyze ATP, GTP, UTP and CTP, and promotes 48S complex formation .
NEW1, helical bundle domain (NEW1_HB)
Type: Domain

This is the helical bundle (HB) domain found in the [NU+] prion formation protein 1 (NEW1) from S. cerevisiae, a translation termination and ribosome biogenesis factor. NEW1 is an ATP binding cassette protein that cosediments with polysomes and is required for biogenesis of the small ribosomal subunit .
AtTam37, zinc finger domain (Zf-AtTam37)
Type: Domain

This domain is found in the AtTam37 (also known as Anu7,

) from Arabidopsis thaliana and related proteins. AtTam37 is an essential component of the chloroplast import motor. It serves as a molecular chaperone within the AtYcf2-FtsHi complex . The domain represented by this entry contains four highly conserved pairs of cysteine residues which are involved in the coordination of two zinc ions.
Nbr1-like, C-terminal UBA domain (UBA_Nbr1_C)
Type: Domain

This UBA domain is found at the C-terminal end of human Next to BRCA1 gene 1 protein (Nbr1) and similar eukaryotic proteins, including JOKA2 from Solanum tuberosum.

Nbr1 (next to BRCA1) is an ubiquitin-binding autophagy adapter that participates in different processes including host defense or intracellular homeostasis . Nbr1-like molecules contain an N-terminal PB1 domain, one (animals, plants) or more (fungi) ZZ domains, an FW domain, and a C-terminal UBA domain .

JOKA2 activates ATG8CL-mediated selective autophagy, and contributes to defense against the fungal pathogen Phytophtora infestans .
AtTam38 (AtTam38)
Type: Family

This entry represents the AtTam38 protein from Arabidopsis thaliana (

) and related plant proteins. AtTam38 is a component of the AtYcf2-FtsHi complex. AtTam38 serves as an anchor of the stromal motor module to the IEM (inner envelope membrane of the chloroplast) . It plays a key role in AtYcf2-FtsHi assembly and maintenance of the tilted posture of the motor module .
AtTam9 (AtTam9)
Type: Family

This entry represents the AtTam9 protein from Arabidopsis thaliana (

) and related plant proteins. AtTam9 is a component of the AtYcf2-FtsHi complex. AtTam9 is a small soluble protein which mainly interacts with the NTD of FtsHi5, another component of the AtYcf2-FtsHi complex, and likely contributes to the local assembly and stability of the complex .
Nonribosomal peptide synthetase sidD, N-terminal (SIDD_N)
Type: Domain

This entry represents the N-terminal domain of SIDD (Nonribosomal peptide synthetase sidD) from Aspergillus fumigatus and related fungal sequences. SIDD is part of the siderophore biosynthetic pathway .
NUP210, fourth Ig-like domain (Ig_NUP210_4th)
Type: Domain

This is the fourth Ig-like domain of NUP210 and its homologues.

NUP210 is essential for nuclear pore assembly and fusion, nuclear pore spacing, as well as for its structural integrity. NUP210 is composed of multiple immunoglobulin-like (Ig-like) domains and forms a ring around the NPC within the NE lumen . There are eight copies of NUP210 per spoke. NUP210 is the only NUP that primarily resides in the NE lumen. This protein is not required for faithful NPC assembly .
NUP210, Ig-like domain 6 (Ig_NUP210_6th)
Type: Domain

This domain is found in human Nuclear pore membrane glycoprotein 210 (NUP210) and similar animal proteins.

NUP210 is essential for nuclear pore assembly and fusion, nuclear pore spacing, as well as for its structural integrity. NUP210 is composed of multiple immunoglobulin-like (Ig-like) domains and forms a ring around the NPC within the NE lumen . There are eight copies of NUP210 per spoke. NUP210 is the only NUP that primarily resides in the NE lumen. This protein is not required for faithful NPC assembly .
NUP210, Ig-like domain 9 (Ig_NUP210_9th)
Type: Domain

This domain is found in human Nuclear pore membrane glycoprotein 210 (NUP210) and similar animal proteins.

NUP210 is essential for nuclear pore assembly and fusion, nuclear pore spacing, as well as for its structural integrity. NUP210 is composed of multiple immunoglobulin-like (Ig-like) domains and forms a ring around the NPC within the NE lumen . There are eight copies of NUP210 per spoke. NUP210 is the only NUP that primarily resides in the NE lumen. This protein is not required for faithful NPC assembly .
COBRA, C-terminal domain (COB_C)
Type: Domain

This entry represents a domain found C-terminal in the COBRA family of proteins from Arabidopsis thaliana and related plant sequences. COBRA family members are all extracellular glycosyl-phosphatidyl inositol-anchored proteins (GPI-linked) . COBRA is involved in determining the orientation of cell expansion, probably by playing an important role in cellulose deposition . The domain represented by this entry is predicted to adopt a β-sandwich fold.
CC142, N-terminal (CC142_N)
Type: Domain

This entry represents the N-terminal coiled-coils of CC142, a protein whose function is still unknown.
YvbJ-like, NTF2-like domain (NTF2_YvbJ)
Type: Domain

This domain is found in Uncharacterized membrane protein YvbJ from Bacillus subtilis and related proteins found in firmicutes. YvbJ is thought to contain a pair of NTF2-like domains toward the C terminus. This domain is the first in the pair.
PA4575-like (PA4575-like)
Type: Family

This entry represents a family of proteins that includes the Pseudomonas aeruginosa protein PA4575 (

). The function of these proteins is unknown.
YMR265C-like, C-terminal (YMR265C_C)
Type: Domain

This is the presumed C-terminal domain of the uncharacterised yeast protein YMR265C, which has a HAD domain (

) at the N-terminal, found in Swiss Army Knife RNA repair proteins. The function of this domain is unknown.
YfjL-like, C-terminal domain (YfjL_C)
Type: Domain

This entry represents the C-terminal domain of the uncharacterised protein YfjL from Bacillus subtilis and similar sequences from firmicutes.
Replication-associated protein ORF2/G2P domain (ORF2/G2P_dom)
Type: Domain

This entry represents a domain found in a group of Replication-associated proteins including ORF2 from Spiroplasma virus 4 (SpV4) and G2P from phages such as Xanthomonas phage phiLf and Bdellovibrio phage phiMH2K. These proteins play an essential role in viral DNA replication; they bind the origin of replication and cleaves the dsDNA replicative form I (RFI) and becomes covalently bound to it via phosphotyrosine bond, generating the dsDNA replicative form II (RFII). After one round of rolling circle synthesis, protein G2P is linked to the newly synthesized ssDNA and joins the ends of the displaced strand to generate a circular single-stranded molecule ready to be packed into a virion.
U3 small nucleolar RNA-associated protein 6 homolog, C-terminal (UTP6_C)
Type: Domain

U3 small nucleolar RNA-associated protein 6 homolog (UTP6) is a component of the small subunit (SSU) processome containing the U3 snoRNA that is involved in processing of pre-18S rRNA . These proteins consist of TPRs; this entry represents the C-terminal region of UTP6 and similar sequences predominantly found in animals and some plant species.
Podophage GP4 fiber I protein gp80-like (Gp80-like)
Type: Family

This entry represents the Podophage GP4 fiber I protein gp80 and related phage and prophage proteins. The structure of gp80 has an unusual barrel-like topology with one strand contributed by the rope protein (

). The N terminus of gp80 folds into an α-helix which is involved in the dimerisation .

Bacteriophage tail fibres play a critical role in the early stage of infection by binding to the bacterial surface. In Podophage GP4, five fibre I, each composed of five dimers of gp80 and linked by rope protein, are attached to the five edges of the tail vertex of the icosahedral head of the phage . The fibre-tail adaptor acts as a fulcrum, encircling the dodecameric adaptor I and providing the anchoring sites for the 5-fold symmetric fibres I and II.
Phage SU10 portal protein (SU10_portal)
Type: Family

This entry represents the portal protein of Escherichia coli phage SU10 and related protein from phages and prophages. The portal protein, encoded by gp6, forms a dodecameric complex that replaces a pentamer of capsid proteins at one vertex of the prolate SU10 capsid (

) . The portal complex enables packaging of the viral genome into the capsid as well as attachment of the phage tail . The portal protein contains wing, stem, clip, crown and barrel domains. The wing domain interacts with the viral DNA and the capsid proteins. The clip domain enables attachment of the adaptor protein complex.
Tricalbin-1-3-like, C2 domain (TCB1-3_C2)
Type: Domain

This entry represents the C2 domain found in Tricalbin-1-3 from Saccharomyces cerevisiae (TCB1-3) and similar fungal proteins. TCB1 may play a role in membrane trafficking . This domain is predicted to form an eight-stranded β-sandwich.
DNA-binding phage zinc finger domain, putative (Phage_Znf_bind_put)
Type: Domain

This entry represents a large family of zinc binding domains that are found in both phage and bacterial proteins. The phage domains tend to be single domain proteins. The bacterial domains are often found in multidomain proteins. Structure predictions suggest this domain may bind to dsDNA. In about quarter of the proteins this domain is found associated with a resolvase domains

found in site specific recombinases.
Phage JBD30-like tail terminator protein-like (Phage_JBD30_tail_term-like)
Type: Family

This entry represents a family of phage tail terminator proteins related to the Pseudomonas aeruginosa phage JBD30 tail terminator protein . These proteins form a hexameric ring at the top of the phage tail tube in the neck of the phage (

). This family also includes proteobacterial prophages.
Trafficking protein particle complex subunit TRAPPC10/Trs130, N-terminal (TRAPPC10/Trs130_N)
Type: Domain

This domain is found at the N-terminal end of human Trafficking protein particle complex subunit 10 (TRAPPC10), yeast Trafficking protein particle complex II-specific subunit 130 (Trs130) and similar eukaryotic proteins. This domain is predicted to adopt an α-β configuration.

The trafficking protein particle complex TRAPP is a multi-protein complex needed in the early stages of the secretory pathway. To date, two kinds of TRAPP complexes have been studied, TRAPPI and TRAPP II. These complexes differ in subunit composition . TRAPP I binds vesicles derived from the endoplasmic reticulum bringing them closer to the acceptor membrane. TRAPPII activates GTPase Ypt31/Ypt32 as the guanine nucleotide exchange factor in the trans-Golgi network to determine the maturation of Golgi cisternae into post-Golgi carriers in yeast .

The TRAPPC10/Trs130 subunit of the TRAPP II complex functions in late Golgi trafficking as a membrane tether. TRAPPII binds the Ypt1 GTPase and probably uses the TRAPPI catalytic core to promote guanine nucleotide exchange. TRS130 plays a role in the YPT GEF activity of TRAPP II .
XM1 gp53 minor capsid protein-like (Gp53-like)
Type: Family

This entry represents a family of phage and bacterial prophage proteins, including

from Myoviridae Phage XM1 (gp53 minor capsid protein). These proteins form a trimeric arrangement which stabilises the phage capsid (

) . They adopt a structure which is known as a β-tulip fold.
Trafficking protein particle complex II-specific subunit 130, second Ig-like domain (Ig_TR130_2nd)
Type: Domain

This domain is found in the yeast Trafficking protein particle complex II-specific subunit 130 (TR130) and related proteins from Saccharomycetes. TRS130 plays a role in the YPT GEF activity of TRAPP II in concert with the two other TRAPP II-specific subunits TRS65 and TRS120. This protein contains four Ig-like domains arranged in tandem . This entry represents the second of these domains.

The trafficking protein particle complex TRAPP is a multi-protein complex needed in the early stages of the secretory pathway. To date, two kinds of TRAPP complexes have been studied, TRAPPI and TRAPP II. These complexes differ in subunit composition . TRAPP I binds vesicles derived from the endoplasmic reticulum bringing them closer to the acceptor membrane. TRAPPII activates GTPase Ypt31/Ypt32 as the guanine nucleotide exchange factor in the trans-Golgi network to determine the maturation of Golgi cisternae into post-Golgi carriers in yeast .

The TRAPPC10/Trs130 subunit of the TRAPP II complex functions in late Golgi trafficking as a membrane tether. TRAPPII binds the Ypt1 GTPase and probably uses the TRAPPI catalytic core to promote guanine nucleotide exchange. TRS130 plays a role in the YPT GEF activity of TRAPP II .
Trafficking protein particle complex II-specific subunit 130, NTS domain (NTS_TR130)
Type: Domain

This domain is found in the yeast Trafficking protein particle complex II-specific subunit 130 (TR130) and related proteins from ascomycetes. TRS130 plays a role in the YPT GEF activity of TRAPP II in concert with the two other TRAPP II-specific subunits TRS65 and TRS120. This protein contains an N-terminal α-solenoid domain, known as NTS domain, followed by four Ig-like domains arranged in tandem . This entry represents the NTS domain.

The trafficking protein particle complex TRAPP is a multi-protein complex needed in the early stages of the secretory pathway. To date, two kinds of TRAPP complexes have been studied, TRAPPI and TRAPP II. These complexes differ in subunit composition . TRAPP I binds vesicles derived from the endoplasmic reticulum bringing them closer to the acceptor membrane. TRAPPII activates GTPase Ypt31/Ypt32 as the guanine nucleotide exchange factor in the trans-Golgi network to determine the maturation of Golgi cisternae into post-Golgi carriers in yeast .

The TRAPPC10/Trs130 subunit of the TRAPP II complex functions in late Golgi trafficking as a membrane tether. TRAPPII binds the Ypt1 GTPase and probably uses the TRAPPI catalytic core to promote guanine nucleotide exchange. TRS130 plays a role in the YPT GEF activity of TRAPP II .
Trafficking protein particle complex subunit 10, immunoglobulin-like (Ig_TRAPPC10)
Type: Domain

This domain is found in human Trafficking protein particle complex subunit 10 (TRAPPC10) and similar proteins specific to animals. TRAPPC10 is a subunit of the TRAPP (transport protein particle) II complex, a highly conserved vesicle tethering complex that functions in late Golgi trafficking as a membrane tether . This domain is predicted to adopt an Immunoglobulin-like (Ig-like) fold.
Octameric membrane protein (8xMP)
Type: Family

This entry represents uncharacterised proteins found in bacteria. They are predicted as integral membrane proteins composed of three integral membrane α-helices. Structure prediction suggests that these proteins form an octameric complex (

ipTM = 0.81 pTM = 0.82). This complex contains a central pore. The predicted complex has a flat face on the predicted extracellular face that suggests it may form a complex with another as yet unidentified partner. The α-helices could project into the cytoplasm.