SII-SWORD/CoKE huggingface dataset:
Extracellular hemoglobin linker subunit, heterodimerisation domain (Extrac_hemoglob_link_heterodim)
Type: Homologous_superfamily

This entry represents the heterodimerisation domain found in extracellular hemoglobin linker subunits. In the earthworm Lumbricus terrestris the linker subunits assemble into a core complex with D(6) symmetry onto which 12 hemoglobin dodecamers bind to form the entire complex .
YvfG domain superfamily (YvfG_sf)
Type: Homologous_superfamily

Yvfg is a hypothetical protein of 71 residues expressed in some bacteria. The monomer consists of two parallel α-helices, and the protein crystallises as a homodimer.
TAFH/NHR1 domain superfamily (TAFH/NHR1_dom_sf)
Type: Homologous_superfamily

The TAF homology (TAFH) or Nervy homology region 1 (NHR1) domain is a domain of 95-100 amino acids present in eukaryotic proteins of the MTG/ETO family and whereof the core ~75-80 residues occur in TAF proteins. The transcription initiation TFIID complex is composed of TATA binding protein (TBP) and a number of TBP-associated factors (TAFs). The TAFH/NHR1 domain is named after fruit fly TATA-box-associated factor 110 (TAF110), human TAF105 and TAF130, and the fruit fly protein Nervy, which is a homologue of human MTG8/ETO . The human eight twenty-one (ETO, MTG8 or CBFA2T1) and related myeloid transforming gene products MTGR1 and MTG16 as well as the Nervy protein contain the NHR1-4 domains. The NHR1/TAFH domain occurs in the N-terminal part of these proteins, while a MYND-type zinc finger forms the NHR4 domain . The TAFH/NHR1 domain can be involved in protein-protein interactions, e.g in MTG8/ETO with HSP90 and Gfi-1 .

Structurally, the TAFH/NHR1 domain consists of five helices with a close folded leaf topology.
NEAT domain superfamily (NEAT_dom_sf)
Type: Homologous_superfamily

This domain superfamily identifies a group of iron-regulated surface determinant proteins found exclusively in bacteria. Among them, the iron-regulated surface determinant protein H (isdH, also known as harA) binds human plasma haptoglobin-hemoglobin complexes, haptoglobin and hemoglobin. It binds haptoglobin-hemoglobin complexes with significantly higher affinity than haptoglobin alone . In Staphylococcus aureus, isdH protein contains three NEAT (NEAr Transporter) domains: IsdH(N1), IsdH(N2), and IsdH(N3). These three domains have different functions, IsdH(N1) binds hemoglobin and haptoglobin, whereas IsdH(N3) captures heme that is released from hemoglobin .
WSSV envelope protein Vp28 superfamily (WSSV_Vp28_sf)
Type: Homologous_superfamily

This superfamily of proteins is found in viruses. Proteins in this superfamily are approximately 210 amino acids in length. There is a conserved NNT sequence motif. These proteins are structural envelope proteins in viruses. This is the β barrel C-terminal domain. There is a protruding N-terminal domain which completes the proteins. Three of four envelope proteins in Shrimp white spot syndrome virus (WSSV) share sequence homology with each other and are present in this superfamily - VP24, VP26 and VP28. VP19 is the other major envelope protein but shares no sequence homology with the other proteins. These proteins are essential for entry into cells of the crustacean host.
Mib/herc2 domain superfamily (Mib_Herc2_sf)
Type: Homologous_superfamily

Mib is a RING ubiquitin ligase in the Notch pathway. Mib interacts with the intracellular domain of Delta to promote its ubiquitylation and internalisation. Cell transplantation studies suggest that mib function is essential in the signalling cell for efficient activation of Notch in neighbouring cells. This domain has been named 'mib/herc2 domain' in and usually the protein also contains an E3 ligase domain (either Ring or Hect).
NRDP1, C-terminal (NRDP1_C)
Type: Homologous_superfamily

This entry represents the C-terminal domain found in E3 ubiquitin-protein ligase NRDP1. It has an α-β-α(3)-β(3) fold with a pseudo barrel β-sheet of an SH3-like topology, surrounded by helices.
ASC domain superfamily (ASC_dom_sf)
Type: Homologous_superfamily

Association with the SNF1 complex (ASC) domain is found in the Sip1/Sip2/Gal83/AMPKbeta subunits of the SNF1/AMP-activated protein kinase (AMPK) complex . SNF1/AMPK are heterotrimeric enzymes composed of a catalytic alpha-subunit, a regulatory gamma-subunit and a regulatory/targeting beta-subunit . Saccharomyces cerevisiae encodes three beta-subunit genes, Sip1, Sip2 and Gal83 . The beta-subunits function as target selective adaptors that recruit the catalytic kinase and regulator Snf4/gamma-subunits. The ASC domain is required for interaction with Snf4 .

The SNF1 kinase complex is required for transcriptional, metabolic, and developmental adaptations in response to glucose limitation . As glucose levels decrease, Snf1 is activated and promotes the use of alternative carbon sources.

Structurally, this domain comprises three short helices and 3-stranded meander β-sheet which makes extensive intermolecular interactions.
Type II secretion system protein GspE, N-terminal superfamily (T2SS_E_N_sf)
Type: Homologous_superfamily

This domain superfamily is found at the N terminus of members of the general secretory system II protein E. Proteins in this subfamily are typically involved in Type IV pilus biogenesis (e.g.

), though some are involved in other processes; for instance aggregation in Myxococcus xanthus (e.g.

) . Its structure contains an extra C-terminal helix that packs against a shorter N-terminal helix.
PB2, C-terminal (PDB2_C)
Type: Homologous_superfamily

Two separate sequences, one N-(242-282) and the other C-terminal (538-577) proximal segments of PB2 subunit, constitute the RNA cap-binding site of the Influenza virus RNA polymerase . This entry represents the C-terminal domain superfamily, its structure consists of an α-β-α-X-α-β(2) fold arranged in three layers (α/β/α) with antiparallel β-sheet, where the connection between helices 2 and 3 runs over the edge of the β-sheet. The C-terminal domain of PB2 forms a stable complex with human importin alpha5 in vitro which, suggests that this domain directs nuclear import. This is further backed by the presence of a previously missed bipartite nuclear localization sequence (NLS) within this domain .
BRK domain superfamily (BRK_sf)
Type: Homologous_superfamily

The function of this domain is unknown . It is often found associated with helicases and transcription factors.
YonK superfamily (YonK_sf)
Type: Homologous_superfamily

YonK protein is expressed by the bacterial prophage SPbetaC . It is a 63 residue protein that associates into a homo-octamer in the form of a β-stranded barrel with four outer helical features at points of the compass. Its function is unknown.
TTHC002-like (TTHC002-like)
Type: Homologous_superfamily

This entry incudes the hypothetical protein TTHC002 from Thermus thermophilus. Its has an α-β-α-β(3) structure and forms a dimer with a single β-sheet, folded in a barrel-like shape.
Phosphoprotein, central domain (Phosphoprotein_central)
Type: Homologous_superfamily

This entry contains the central domain of the phosphoprotein from vesiculoviruses, which are ssRNA negative-strand rhabdoviruses. It is known as the phosphoprotein or P protein . This protein may be part of the RNA dependent RNA polymerase complex . The phosphorylation states of this protein may regulate the transcription and replication complexes .

The structure of this domain consists of an intertwinned homodimer of β(2)-α-β(2) motifs arranged in three layers (β/α/β); each antiparallel β-sheet is formed by the N-terminal β-hairpin of one subunit and the C-terminal β-hairpin of the other subunit.
TFIID subunit TAF5, NTD2 domain superfamily (TFIID_NTD2_sf)
Type: Homologous_superfamily

This region is an all-alpha domain associated with the WD40 helical bundle of the TAF5 subunit of transcription factor TFIID. The domain has distant structural similarity to RNA polymerase II CTD interacting factors. It contains several conserved clefts that are likely to be critical for TFIID complex assembly . The TAF5 subunit is present twice in the TFIID complex and is critical for the function and assembly of the complex, and the NTD2 (second N-terminal domain) and N-terminal domain are crucial for homodimerisation . TAF5 has a paralogue gene (TAF5L) which has a redundant function .

The TATA Binding Protein (TBP) Associated Factor 5 (TAF5) is one of several TAFs that bind TBP and are involved in forming Transcription Factor IID (TFIID) complex. TFIID plays an important role in the recognition of promoter DNA and assembly of the preinitiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. In yeast and human cells, TAFs have been found as components of other complexes besides TFIID .

The N-terminal domain of TAF5 has a multihelical structure with a C-terminal β-α(2)-β motif, one central buried helix and parallel β-ribbon.

This domain is also found in the so-called 'Protein will decrease acetylation' from Drosophila melanogaster which is a component of the transcription regulatory complex SAGA, a multiprotein complex that activates transcription by remodeling chromatin and mediating histone acetylation and deubiquitination [

,

,

.
Poly(A) polymerase catalytic subunit superfamily (PolyA_pol_cat_sf)
Type: Homologous_superfamily

Poly(A) polymerase (

) catalyses template-independent extension of the 3'-end of a DNA or RNA strand by one nucleotide at a time. The Poxvirus enzyme creates the 3'(poly)A tail of mRNAs, and is a heterodimer of a catalytic and a regulatory subunit. This is the catalytic subunit.

Structurally, the catalytic subunit consists of three domains. The first domain has an all-α fold and contains a HhH motif. The second domain has an α+β fold, distantly related to the nucleotidyltransferase superfamily (

). The third domain has a β(3)-α-β(3)-α(2) fold arranged in three layers (α/β/α) with mixed β-sheet of six strands where strands 2 and 5 are antiparallel to the rest.
Photosystem II PsbL superfamily (PSII_PsbL_sf)
Type: Homologous_superfamily

Oxygenic photosynthesis uses two multi-subunit photosystems (I and II) located in the cell membranes of cyanobacteria and in the thylakoid membranes of chloroplasts in plants and algae. Photosystem II (PSII) has a P680 reaction centre containing chlorophyll 'a' that uses light energy to carry out the oxidation (splitting) of water molecules, and to produce ATP via a proton pump. Photosystem I (PSI) has a P700 reaction centre containing chlorophyll that takes the electron and associated hydrogen donated from PSII to reduce NADP+ to NADPH. Both ATP and NADPH are subsequently used in the light-independent reactions to convert carbon dioxide to glucose using the hydrogen atom extracted from water by PSII, releasing oxygen as a by-product .

PSII is a multisubunit protein-pigment complex containing polypeptides both intrinsic and extrinsic to the photosynthetic membrane . Within the core of the complex, the chlorophyll and β-carotene pigments are mainly bound to the antenna proteins CP43 (PsbC) and CP47 (PsbB), which pass the excitation energy on to the reaction centre proteins D1 (Qb, PsbA) and D2 (Qa, PsbD) that bind all the redox-active cofactors involved in the energy conversion process. The PSII oxygen-evolving complex (OEC) oxidises water to provide protons for use by PSI, and consists of OEE1 (PsbO), OEE2 (PsbP) and OEE3 (PsbQ). The remaining subunits in PSII are of low molecular weight (less than 10kDa), and are involved in PSII assembly, stabilisation, dimerisation, and photo-protection .

This entry represents the low molecular weight transmembrane protein PsbL found in PSII. PsbL is located in a gene cluster with PsbE, PsbF and PsbJ (PsbEFJL). Both PsbL and PsbJ (

) are essential for proper assembly of the OEC. Mutations in PsbL prevent the formation of both PSII core dimers and PSII-light harvesting complex . In addition, both PsbL and PsbJ are involved in the unidirectional flow of electrons, where PsbJ regulates the forward electron flow from D2 (Qa) to the plastoquinone pool, and PsbL prevents the reduction of PSII by back electron flow from plastoquinol protecting PSII from photo-inactivation .
Photosystem II PsbJ superfamily (PSII_PsbJ_sf)
Type: Homologous_superfamily

Oxygenic photosynthesis uses two multi-subunit photosystems (I and II) located in the cell membranes of cyanobacteria and in the thylakoid membranes of chloroplasts in plants and algae. Photosystem II (PSII) has a P680 reaction centre containing chlorophyll 'a' that uses light energy to carry out the oxidation (splitting) of water molecules, and to produce ATP via a proton pump. Photosystem I (PSI) has a P700 reaction centre containing chlorophyll that takes the electron and associated hydrogen donated from PSII to reduce NADP+ to NADPH. Both ATP and NADPH are subsequently used in the light-independent reactions to convert carbon dioxide to glucose using the hydrogen atom extracted from water by PSII, releasing oxygen as a by-product .

PSII is a multisubunit protein-pigment complex containing polypeptides both intrinsic and extrinsic to the photosynthetic membrane . Within the core of the complex, the chlorophyll and β-carotene pigments are mainly bound to the antenna proteins CP43 (PsbC) and CP47 (PsbB), which pass the excitation energy on to the reaction centre proteins D1 (Qb, PsbA) and D2 (Qa, PsbD) that bind all the redox-active cofactors involved in the energy conversion process. The PSII oxygen-evolving complex (OEC) oxidises water to provide protons for use by PSI, and consists of OEE1 (PsbO), OEE2 (PsbP) and OEE3 (PsbQ). The remaining subunits in PSII are of low molecular weight (less than 10kDa), and are involved in PSII assembly, stabilisation, dimerisation, and photo-protection .

This entry represents the low molecular weight transmembrane protein PsbJ found in PSII. PsbJ is one of the most hydrophobic proteins in the thylakoid membrane, and is located in a gene cluster with PsbE, PsbF and PsbL (PsbEFJL). Both PsbJ and PsbL (

) are essential for proper assembly of the OEC. Mutations in PsbJ cause the light-harvesting antenna to remain detached from the PSII dimers . In addition, both PsbJ and PsbL are involved in the unidirectional flow of electrons, where PsbJ regulates the forward electron flow from D2 (Qa) to the plastoquinone pool, and PsbL prevents the reduction of PSII by back electron flow from plastoquinol protecting PSII from photo-inactivation .
Photosystem II PsbT superfamily (PSII_PsbT_sf)
Type: Homologous_superfamily

Oxygenic photosynthesis uses two multi-subunit photosystems (I and II) located in the cell membranes of cyanobacteria and in the thylakoid membranes of chloroplasts in plants and algae. Photosystem II (PSII) has a P680 reaction centre containing chlorophyll 'a' that uses light energy to carry out the oxidation (splitting) of water molecules, and to produce ATP via a proton pump. Photosystem I (PSI) has a P700 reaction centre containing chlorophyll that takes the electron and associated hydrogen donated from PSII to reduce NADP+ to NADPH. Both ATP and NADPH are subsequently used in the light-independent reactions to convert carbon dioxide to glucose using the hydrogen atom extracted from water by PSII, releasing oxygen as a by-product .

PSII is a multisubunit protein-pigment complex containing polypeptides both intrinsic and extrinsic to the photosynthetic membrane . Within the core of the complex, the chlorophyll and β-carotene pigments are mainly bound to the antenna proteins CP43 (PsbC) and CP47 (PsbB), which pass the excitation energy on to the reaction centre proteins D1 (Qb, PsbA) and D2 (Qa, PsbD) that bind all the redox-active cofactors involved in the energy conversion process. The PSII oxygen-evolving complex (OEC) oxidises water to provide protons for use by PSI, and consists of OEE1 (PsbO), OEE2 (PsbP) and OEE3 (PsbQ). The remaining subunits in PSII are of low molecular weight (less than 10kDa), and are involved in PSII assembly, stabilisation, dimerisation, and photo-protection .

This entry represents the low molecular weight transmembrane protein PsbT found in PSII, which is thought to be associated with the D1 (PsbA) -D2 (PsbD) heterodimer. PsbT may be involved in the formation and/or stabilisation of dimeric PSII complexes, because in the absence of this protein dimeric PSII complexes were found to be less abundant. Furthermore, although PsbT does not confer photo-protection, it is required for the efficient recovery of photo-damaged PSII .
Photosystem II PsbM superfamily (PSII_PsbM_sf)
Type: Homologous_superfamily

Oxygenic photosynthesis uses two multi-subunit photosystems (I and II) located in the cell membranes of cyanobacteria and in the thylakoid membranes of chloroplasts in plants and algae. Photosystem II (PSII) has a P680 reaction centre containing chlorophyll 'a' that uses light energy to carry out the oxidation (splitting) of water molecules, and to produce ATP via a proton pump. Photosystem I (PSI) has a P700 reaction centre containing chlorophyll that takes the electron and associated hydrogen donated from PSII to reduce NADP+ to NADPH. Both ATP and NADPH are subsequently used in the light-independent reactions to convert carbon dioxide to glucose using the hydrogen atom extracted from water by PSII, releasing oxygen as a by-product .

PSII is a multisubunit protein-pigment complex containing polypeptides both intrinsic and extrinsic to the photosynthetic membrane . Within the core of the complex, the chlorophyll and β-carotene pigments are mainly bound to the antenna proteins CP43 (PsbC) and CP47 (PsbB), which pass the excitation energy on to the reaction centre proteins D1 (Qb, PsbA) and D2 (Qa, PsbD) that bind all the redox-active cofactors involved in the energy conversion process. The PSII oxygen-evolving complex (OEC) oxidises water to provide protons for use by PSI, and consists of OEE1 (PsbO), OEE2 (PsbP) and OEE3 (PsbQ). The remaining subunits in PSII are of low molecular weight (less than 10kDa), and are involved in PSII assembly, stabilisation, dimerisation, and photo-protection .

This entry represents the low molecular weight transmembrane protein PsbM found in PSII. PsbM is one of the most hydrophobic proteins in the thylakoid membrane. The function of this protein is unknown.
Photosystem II PsbK superfamily (PSII_PsbK_sf)
Type: Homologous_superfamily

Oxygenic photosynthesis uses two multi-subunit photosystems (I and II) located in the cell membranes of cyanobacteria and in the thylakoid membranes of chloroplasts in plants and algae. Photosystem II (PSII) has a P680 reaction centre containing chlorophyll 'a' that uses light energy to carry out the oxidation (splitting) of water molecules, and to produce ATP via a proton pump. Photosystem I (PSI) has a P700 reaction centre containing chlorophyll that takes the electron and associated hydrogen donated from PSII to reduce NADP+ to NADPH. Both ATP and NADPH are subsequently used in the light-independent reactions to convert carbon dioxide to glucose using the hydrogen atom extracted from water by PSII, releasing oxygen as a by-product .

PSII is a multisubunit protein-pigment complex containing polypeptides both intrinsic and extrinsic to the photosynthetic membrane . Within the core of the complex, the chlorophyll and β-carotene pigments are mainly bound to the antenna proteins CP43 (PsbC) and CP47 (PsbB), which pass the excitation energy on to the reaction centre proteins D1 (Qb, PsbA) and D2 (Qa, PsbD) that bind all the redox-active cofactors involved in the energy conversion process. The PSII oxygen-evolving complex (OEC) oxidises water to provide protons for use by PSI, and consists of OEE1 (PsbO), OEE2 (PsbP) and OEE3 (PsbQ). The remaining subunits in PSII are of low molecular weight (less than 10kDa), and are involved in PSII assembly, stabilisation, dimerisation, and photo-protection .

This entry represents the low molecular weight transmembrane protein PsbK found in PSII, where it is tightly associated with the antenna protein CP43 (PsbC). PsbK is required for accumulation of the PSII complex, and may participate in the assembly and stability of the PSII complex. In particular, PsbK may be involved in the binding of plastoquinone and in maintaining the dimeric organisation of PSII .
Photosystem II PsbI superfamily (PSII_PsbI_sf)
Type: Homologous_superfamily

Oxygenic photosynthesis uses two multi-subunit photosystems (I and II) located in the cell membranes of cyanobacteria and in the thylakoid membranes of chloroplasts in plants and algae. Photosystem II (PSII) has a P680 reaction centre containing chlorophyll 'a' that uses light energy to carry out the oxidation (splitting) of water molecules, and to produce ATP via a proton pump. Photosystem I (PSI) has a P700 reaction centre containing chlorophyll that takes the electron and associated hydrogen donated from PSII to reduce NADP+ to NADPH. Both ATP and NADPH are subsequently used in the light-independent reactions to convert carbon dioxide to glucose using the hydrogen atom extracted from water by PSII, releasing oxygen as a by-product .

PSII is a multisubunit protein-pigment complex containing polypeptides both intrinsic and extrinsic to the photosynthetic membrane . Within the core of the complex, the chlorophyll and β-carotene pigments are mainly bound to the antenna proteins CP43 (PsbC) and CP47 (PsbB), which pass the excitation energy on to the reaction centre proteins D1 (Qb, PsbA) and D2 (Qa, PsbD) that bind all the redox-active cofactors involved in the energy conversion process. The PSII oxygen-evolving complex (OEC) oxidises water to provide protons for use by PSI, and consists of OEE1 (PsbO), OEE2 (PsbP) and OEE3 (PsbQ). The remaining subunits in PSII are of low molecular weight (less than 10kDa), and are involved in PSII assembly, stabilisation, dimerisation, and photo-protection .

This entry represents the low molecular weight transmembrane protein PsbI, which is tightly associated with the D1/D2 heterodimer in PSII. The function of PsbI is unknown, but it may be involved in the assembly, dimerisation or stabilisation of PSII dimers .
Sodium:neurotransmitter symporter superfamily (SNS_sf)
Type: Homologous_superfamily

Neurotransmitter transport systems are integral to the release, re-uptake and recycling of neurotransmitters at synapses. High affinity transport proteins found in the plasma membrane of presynaptic nerve terminals and glial cells are responsible for the removal from the extracellular space of released-transmitters, thereby terminating their actions . Plasma membrane neurotransmitter transporters fall into two structurally and mechanistically distinct families. The majority of the transporters constitute an extensive family of homologous proteins that derive energy from the co-transport of Na
+
and Cl
-
, in order to transport neurotransmitter molecules into the cell against their concentration gradient. The family has a common structure of 12 presumed transmembrane helices and includes carriers for gamma-aminobutyric acid (GABA), noradrenaline/adrenaline, dopamine, serotonin, proline, glycine, choline, betaine and taurine. They are structurally distinct from the second more-restricted family of plasma membrane transporters, which are responsible for excitatory amino acid transport. The latter couple glutamate and aspartate uptake to the cotransport of Na
+
and the counter-transport of K
+
, with no apparent dependence on Cl
-
. In addition, both of these transporter families are distinct from the vesicular neurotransmitter transporters .