SII-SWORD/CoKE huggingface dataset:
RNA-directed RNA polymerase, C-terminal, birnavirus (Birnavirus_RdRp_C)
Type: Domain

RNA-directed RNA polymerase (RdRp) (

) is an essential protein encoded in the genomes of all RNA containing viruses with no DNA stage . It catalyses synthesis of the RNA strand complementary to a given RNA template, but the precise molecular mechanism remains unclear.
The postulated RNA replication process is a two-step mechanism. First, the initiation step of RNA synthesis begins at or near the 3' end of the RNA template by means of a primer-independent (de novo) mechanism. The de novo initiation consists in the addition of a nucleotide tri-phosphate (NTP) to the 3'-OH of the first initiating NTP. During the following so-called elongation phase, this nucleotidyl transfer reaction is repeated with subsequent NTPs to generate the complementary RNA product .

This entry represents the C-terminal domain of RdRp from Birnavirus, which lack the highly conserved Gly-Asp-Asp (GDD) sequence, a component of the proposed catalytic site of this enzyme family that exists in the conserved motif VI of the palm domain (

) of other RdRps . These enzymes have the five essential RNA polymerase motifs in a permuted order of C-A-B-D-E to form a conserved catalytic active site . This domain is mostly α-helical and runs across the canyon in the front of the palm, wrapping around the fingers subdomain , which may function to prevent back-primed RNA synthesis during protein priming.
Thioester domain 2 (TED_2)
Type: Domain

This entry represents a domain that is related to the TED domain (

). It is found in bacterial proteins.
RNA-directed RNA polymerase, thumb domain, birnavirus (Birnavirus_RdRp_thumb)
Type: Domain

RNA-directed RNA polymerase (RdRp) (

) is an essential protein encoded in the genomes of all RNA containing viruses with no DNA stage . It catalyses synthesis of the RNA strand complementary to a given RNA template, but the precise molecular mechanism remains unclear.
The postulated RNA replication process is a two-step mechanism. First, the initiation step of RNA synthesis begins at or near the 3' end of the RNA template by means of a primer-independent (de novo) mechanism. The de novo initiation consists in the addition of a nucleotide tri-phosphate (NTP) to the 3'-OH of the first initiating NTP. During the following so-called elongation phase, this nucleotidyl transfer reaction is repeated with subsequent NTPs to generate the complementary RNA product .

This entry represents the thumb domain of RdRp from Birnavirus, which contain the conserved RdRp motifs that reside in the catalytic "palm" domain (

) of all classes of polymerases but in a characteristic permuted order, thus, it adopts a unique active site topology . Additionally, the birnavirus RdRps lack the highly conserved Gly-Asp-Asp (GDD) sequence, a component of the proposed catalytic site of this enzyme family that exists in the conserved motif VI of the palm domain of other RdRps .
Torsin-1A-interacting protein 1/2, AAA+ activator domain (TOIP1/2_C)
Type: Domain

This entry represents the C-terminal AAA+ activator domain of Torsin-1A-interacting proteins 1 and 2 (TOIP1/2) also known as LAP1 proteins (Lamina-associated polypeptide 1), which are type 2 integral membrane proteins with a single membrane-spanning region of the inner nuclear membrane . These proteins interact with and activate Torsin A, an AAA+ ATPase localized to the endoplasmic reticulum (ER), through a perinuclear domain and forms a heterohexameric (LAP1-Torsin)3 ring that targets Torsin to the nuclear envelope. LAP1 has an atypical AAA+ fold and provides an arginine finger to the Torsin A active site to promote its ATPase activity . A single mutation in Torsin A causes early onset primary dystonia, a painful and severely disabling neuromuscular disease .
Torsin-1A-interacting protein 1/2, N-terminal (TOIP1/2_N)
Type: Domain

This entry represents the N-terminal domain of Torsin-1A-interacting proteins 1 and 2 (TOIP1/2) also known as LAP1 proteins (Lamina-associated polypeptide 1), which are type 2 integral membrane proteins with a single membrane-spanning region of the inner nuclear membrane . These proteins interact with and activate Torsin A, an AAA ATPase localized to the endoplasmic reticulum (ER), through a perinuclear domain and forms a heterohexameric (LAP1-Torsin)3 ring that targets Torsin to the nuclear envelope. TOIP1/2 has an atypical AAA fold and provides an arginine finger to the Torsin A active site to promote its ATPase activity . A single mutation in Torsin A causes early onset primary dystonia, a painful and severely disabling neuromuscular disease . This domain contains transmembrane helices.
V-type proton ATPase subunit S1, luminal domain (VAS1_LD)
Type: Domain

This entry represents the luminal domain (LD) found in eukaryotic V-type proton ATPase subunit S1 (VAS1), involved in V-ATPase V0 assembly, also known as Ac45 subunit (ATP6AP1) . This domain folds as a globular β-prism structure which is structurally similar to LAMP1-3, thus, the LD domain of Ac45 is an evolutionarily conserved member of the LAMP family . Ac45 is an ER membrane protein that guides the V-type ATPase into specialised subcellular compartments and is critical for Vo complex assembly as it connects to multiple Vo subunits and phospholipids in the c-ring . Missense mutations in the X-linked ATP6AP1 gene cause immunodeficiency in males that leads to recurrent bacterial infection, hepatopathy, cognitive impairment, and abnormal protein glycosylation .
V-type proton ATPase subunit S1/VOA1, transmembrane domain (VAS1/VOA1_TM)
Type: Domain

This entry represents the transmembrane domain from ER/Golgi membrane proteins including V-type proton ATPase subunit S1 V0 complex accessory subunit Ac45 (VAS1, also known as V0 complex accessory subunit Ac45, ATP6AP1) from animals and the yeast homologue V0 assembly protein 1 (VOA1) which are essential for V0 ATPase assembly, stability and function . In humans, mutations of ATP6AP1 cause immunodeficiency with hypogammaglobulinemia, hepatopathy and neurocognitive abnormalities . This entry also includes ER membrane BIG1 proteins from yeast, involved in cell wall biogenesis.
Vps72/YL1, N-terminal (YL1_N)
Type: Domain

This entry include a group of proteins involved in chromatin remodelling, including Vps72 (vacuolar protein sorting-associated protein 72) from budding yeasts. Vps72 is a Htz1-binding component of the SWR1 complex, which is required for the incorporation of the histone variant H2AZ into chromatin . It is also required for vacuolar protein sorting in budding yeasts .

The Vps72 homologue from animals, YL-1, is a deposition-and-exchange histone chaperone specific for H2AZ1, specifically chaperones H2AZ1 and deposits it into nucleosomes. It is component of the SRCAP and Tip60 complexes, and mediates the ATP-dependent exchange of histone H2AZ1/H2B dimers for nucleosomal H2A/H2B, leading to transcriptional regulation of selected genes by chromatin remodeling .

This is the N-terminal region from Vps72/YL1, which covers the aspartate- and glutamate-rich N-terminal domain and the central DNA-binding domain .
Sey1/RHD3-like, three-helix bundle domain (Sey1/RHD3-like_3HB)
Type: Domain

This is the three-helix bundle (3HB) domain found at the C-terminal of Sey1 from yeast and Root hair defective 3 (RHD3) from Arabidopsis, GTP-binding proteins involved in homotypic membrane fusion of the endoplasmic reticulum . This is a stalk-like domain composed of four 3HBs that interacts with its own GTPase domain and that of a neighbouring molecule, to undergo major conformational changes during the GTP cycle to drive membrane fusion .
RNA-binding protein Tab2-like, N-terminal (Tab2-like_N)
Type: Domain

This entry represents the N-terminal domain of proteins from photosynthetic organisms including plants and cyanobacteria, such as Tab2 proteins. Tab2 was first identified in Chlamydomonas reinhardtii as a RNA binding protein required for translation of the chloroplast PsaB photosystem I subunit . Later, the Tab2 homologue (ATAB2) from Arabidopsis was found involved in the signalling pathway of light-controlled synthesis of photosystem proteins during early plant development , presumably functioning as an activator of translation with targets at PSI and PSII .
RNA-binding protein Tab2/Atab2, C-terminal (Tab2-like_C)
Type: Domain

This entry represents the C-terminal domain of Tab2 from plants and cyanobacteria. Tab2 was first identified in Chlamydomonas reinhardtii ([swissprot]:Q7X8Y6) as a RNA-binding protein required for translation of the chloroplast PsaB photosystem I subunit . Later, the Tab2 homologue from Arabidopsis (ATAB2) was found involved in the signalling pathway of light-controlled synthesis of photosystem proteins during early plant development, presumably functioning as an activator of translation with targets at PSI and PSII . Directed mutagenesis experiments carried out in Tab2 from C.reinhardtii indicated the importance of a highly conserved C-terminal tripeptide WLL for normal psaB translation .
Putative adhesive domain (group 17) (pAdhesive_17)
Type: Domain

The structure model of this domain folds into 10 β-strands arranged in two β-sheets as well as 4-5 elongated α-helices. The β-sheets distantly resemble the Collagen_bind (

) domain. It is annotated N-terminal to repeating stalk domains in bacterial surface proteins. This domain can be found on a E. faecalis protein encoded by the EF3314 gene, which was proposed to contribute to the interaction of E. faecalis with the host and to the bacterial virulence .
Phage tail tube protein, C-terminal (Phage_tube_C)
Type: Domain

This entry represents a short all-β domain found at the C-terminal of some phage tube proteins, including Tail tube protein from Lactococcus phage p2, which forms the cylindrical rigid tail tube with a 4 nm wide central channel for DNA ejection. This domain probably makes protruding decorations on the whole length of the tail tube . It is also found in bacterial prophages.
Phage tail tube protein, N-terminal (L_lac_phage_MSP_N)
Type: Domain

This domain is found at the N-terminal of Siphoviridae phage tail tube proteins . This entry also includes some prophages from Firmicutes.
Antitoxin-like, ribbon-helix-helix (Antitox_RHH)
Type: Domain

This presumed domain is found in bacteria, and is approximately 60 amino acids in length. Structure prediction suggests that it has a ribbon-helix-helix motif, a DNA-binding motif commonly found in antitoxin families . Members containing this domain may be related to CopG antitoxin family.
Bacterial hydrolase (Bact_hydrolase)
Type: Family

This family of proteins, found in bacteria and archaea, is thought to have hydrolase activity.
Putative adhesive domain (group 8) (pAdhesive_8)
Type: Domain

The structure model of this domain resembles the C-terminal domains of the Streptococcus intermedius antigen I/II (AgI/II). The N-terminal domain of AgI/II (also called adhesin P1, antigen B or PAc) folds towards the stalk, where it gets locked in place . Given that this domain is found N-terminal to repeating stalk domains in bacterial surface proteins, the domain is suggested to have a potential protein binding function.
Exodeoxyribonuclease X-like, C-terminal (ExoX-like_C)
Type: Domain

This entry represents a short domain found at the C-terminal of Exodeoxyribonuclease 10 (ExoX) from Escherichia coli (strain K12) whose function is unknown. This domain is found in bacteria and some uncharacterised sequences from eukaryotes. There is a conserved FGKY/H sequence motif.
DOCKER, Lobe A (DOCKER_Lobe_A)
Type: Domain

This entry represents a conserved region within a number of eukaryotic dedicator of cytokinesis proteins (DOCK), which are guanine nucleotide exchange factors (GEFs) , that activate some small GTPases by exchanging bound GDP for free GTP such as Rac. DOCK proteins are required during several cellular processes, such as cell motility and phagocytosis . These proteins have a DOCK-homology region 1 (DHR-1, also known as DOCK-type C2 domain) at the N-terminal and a DHR-2 (also known as DOCKER domain) at the C-terminal. The DOCKER domain (

) is a GEF catalytic domain organised into three lobes, A, B and C, with the Rho-family binding site and catalytic centre generated entirely from lobes B and C. This entry represents Lobe A, formed from an antiparallel array of α-helices that adopts a tetratricopeptide repeat-like fold, which through extensive contacts with lobe B, stabilises DHR-2 domain .
DOCKER, Lobe B (DOCKER_Lobe_B)
Type: Domain

This entry represents a conserved region within a number of eukaryotic dedicator of cytokinesis proteins (DOCK), which are guanine nucleotide exchange factors (GEFs) , that activate some small GTPases by exchanging bound GDP for free GTP such as Rac. DOCK proteins are required during several cellular processes, such as cell motility and phagocytosis . These proteins have a DOCK-homology region 1 (DHR-1, also known as DOCK-type C2 domain) at the N-terminal and a DHR-2 (also known as DOCKER domain) at the C-terminal. The DOCKER domain (

) is a GEF catalytic domain organised into three lobes, A, B and C, with the Rho-family binding site and catalytic centre generated entirely from lobes B and C. This entry represents Lobe B, which adopts an unusual architecture of two antiparallel β-sheets disposed in a loosely packed orthogonal arrangement. This lobe changes its position relative to lobe C and the bound GTPase, which suggests that lobe B distinguishes between the switch 1 conformations of the small GTPases Rac1 and Cdc42 .
Putative adhesive domain (group 11) (pAdhesive_11)
Type: Domain

This entry represents a domain found N-terminal to repeating stalk domains in Firmicutes surface proteins. The structure model resembles a receptor binding domain in cattle suggesting protein binding function. The structure model also resembles partly a galactose binding Yersinia pestis antigen.
Putative adhesive domain (group 6) (pAdhesive_6)
Type: Domain

This entry represents a domain that resembles the SdrG_C_C adhesive domain, known to bind within a supra-domain with the SDR-like Ig domain (

) to fibrinogen. It is found N-terminal to repeating stalk domains in bacterial surface proteins.
DOCKER, Lobe C (DOCKER_Lobe_C)
Type: Domain

This entry represents a conserved region within a number of eukaryotic dedicator of cytokinesis proteins (DOCK), which are guanine nucleotide exchange factors (GEFs) , that activate some small GTPases by exchanging bound GDP for free GTP such as Rac. DOCK proteins are required during several cellular processes, such as cell motility and phagocytosis . These proteins have a DOCK-homology region 1 (DHR-1, also known as DOCK-type C2 domain) at the N-terminal and a DHR-2 (also known as DOCKER domain) at the C-terminal. The DOCKER domain (

) is a GEF catalytic domain organised into three lobes, A, B and C, with the Rho-family binding site and catalytic centre generated entirely from lobes B and C. This entry represents Lobe C, which form an antiparallel four α-helical bundle and contains a loop known as the nucleotide sensor characterised by a conserved valine residue essential for catalytic activity .
Putative adhesin domain (group 10) (pAdhesive_10)
Type: Domain

This entry represents a domain found N-terminal to repeating stalk domains in bacterial surface proteins. The structure model of this domain consists out of seven β-strands within two β-sheets, similar to the RrgB pilus backbone, which was again described to correspond to the collagen binding domain. The position of this domain at the tip of bacterial surface proteins suggests an adhesive function.
Cyclin-D-binding Myb-like transcription factor 1, N-terminal (DMTF1_N)
Type: Domain

This domain is found at the N-terminal of Cyclin-D-binding Myb-like transcription factor 1 (DMTF1), which is rich in acidic residues , adjacent

. DMTF1 is a tumour suppressor that interacts with and activates CDKN2A/ARF in response to Ras-Raf signalling, thus inducing p53-dependent cell cycle arrest .
Putative pectate lyase-like adhesive domain (Pectate_lyase_5)
Type: Repeat

This putative domain is found at the N-terminal of a large number of bacterial proteins. Its adhesive function was described in Lactobacillus reuteri serine-rich repeat proteins . Structure predictions show it is composed of a β-solenoid repeat related to Pectate lyase.
GvpD, basic region 2 (GvpD_bR2)
Type: Domain

This entry represents the C-terminal domain of GvpD, which contains the second basic region (bR2, arginine-rich) that may be important for its function .

GvpD is involved in the regulation of gas vesicle formation through the interaction and breakdown induction of the transcriptional activator GvpE .
UPF0758, N-terminal (UPF0758_N)
Type: Domain

This domain is functionally uncharacterised, found at the N-terminal of the uncharacterised UPF0758 proteins from bacteria and archaea, and is approximately 90 amino acids in length. UPF0758 was previously known as the radC family, a name that was assigned according to the radC102 mutant of E. coli which was later demonstrated to be an allele of the transcription-repair-coupling factor recG . UPF0758 has been described as a putative JAMM-family deubiquitinating enzyme, but its function remains to be determined . Structure prediction using Colab notebook from AlphaFold DB suggests that it has an α-bundle fold. It may contain two helix-hairpin-helix (HhH) motifs. This domain is found in association with

.
LapA adhesin domain (LapA_adhesin_dom)
Type: Domain

This Ig-like domain is found repeated in the LapA adhesin found in pseudomonas species. This domain is likely calcium binding and distantly related to the CalX-beta domain

.
Atrophied bacterial Ig domain (aBig_2)
Type: Domain

This domain is related to

, a bacterial immunoglobulin-like domain. It is found centrally in Alpha-L-arabinofuranosidase from Bifidobacterium longum, which plays a role in the type II arabinogalactan (AG) side chains degradation . According to structure predictions members of this group have lost several β-strands found on one sheet of the Ig domain. This domain is found in a wide range of bacterial cell surface proteins.
Phage ORF5 protein (Phage_ORF5)
Type: Family

This family of proteins is found in bacteriophages such as Bacteriophage phiMH2K and Bacteriophage Chp1. Proteins in this family are typically between 81 and 96 amino acids in length. These proteins appear to have a role in phage packaging.
HEWD domain (HEWD)
Type: Domain

This entry represents a small domain found in archaeal proteins that is functionally uncharacterised. There is a conserved HEWD sequence after which the domain is named.
Helix-turn-helix protein, archaea (HTH_63)
Type: Family

This family of proteins is functionally uncharacterised. This family of proteins is found in archaea; they are typically between 161 and 201 amino acids in length. This family shares similarity with

, suggesting it is a transcriptional regulatory protein.
eIF4E-associated protein (Eap1)
Type: Family

This entry represents eIF4E-associated protein (Eap1) from yeast, which plays a role in cell growth and is implicated in the TOR signaling cascade. Eap1 binds to eIF4E and regulates translation. It competes with eIF4G (the large subunit of the cap-binding complex, eukaryotic initiation factor 4F (eIF4F)) for binding to eIF4E and accelerates mRNA degradation by promoting decapping . It associates with Puf5p and Dhh1p, being essential for Puf5p mediated repression .
SrpA-like, SigLec-like domain (SrpA-like_SigLec-like_dom)
Type: Domain

This entry represents a domain found at the N-terminal end of platelet-binding glycoprotein from Streptococcus sanguinis (SrpA), Streptococcal hemagglutinin from Streptococcus gordonii (Hsa) and other proteins from Firmicutes and Actinobacteria. These proteins are involved in hemagglutination and adherence to ghst glycoproteins . This entry includes a Thr-Arg motif conserved across homologous carbohydrate-binding adhesins that may orient the sialic acid moiety of carbohydrate ligands .
Motility protein A, N-terminal (MotA_N)
Type: Domain

This entry represents the N-terminal domain of Motility protein A (MotA). MotA is a membrane protein that forms the stator element of the flagellar motor complex together with MotB with 5:2 stoichiometry, which couples ion flow across the cytoplasmic membrane to generate torque, and thus, it is required for rotation of the flagellar motor. This domain contains conserved torque-generating charged residues at the C-terminal and is adjacent

, which represents MotA, TMH3 and TMH4.
Putative DnaT-like domain (DnaT_2)
Type: Domain

This presumed domain is functionally uncharacterised. This domain is found in bacteria and viruses, and is approximately 110 amino acids in length. This domain is predicted to contain a complex four helical bundle structure. The structure shows similarity to the single stranded DNA-binding protein DnaT.
Putative O-methyltransferase (Methyltransf_35)
Type: Family

This family of bacterial proteins is functionally uncharacterised. An AlphaFold model shows this family is similar to known O-methyltransferases.
Recombinase-like (HTH_62)
Type: Domain

This entry represents a group of bacterial proteins that is functionally uncharacterised. It covers a region that show similarity to the HTH domain of recombinases

.
KBTB, W-type LIR motif (KBTB_W-LIR)
Type: Conserved_site

LC3 Interacting Regions (LIRs), also known as ATG8-interacting motifs (AIMs), are short-linear motifs (SLiMs) of autophagy receptors and adaptor proteins that facilitates the selective recruitment of autophagy substrates to the autophagosome. ATG8 proteins are highly conserved in eukaryotes and play a key role in selective autophagy as they recognise and bind different autophagy receptors and adaptors containing a specific class of SLiMs. LIRs are characterised by degenerated sequences with a four-residue core central sequence involved in ATG8-binding, with the W/Y/FxxL/I/V pattern. Based on the aromatic amino acid in position 1 they can be classified into W-type, Y-type and F-type. This entry represents the W-type LIR motif from Kelch repeat and BTB domain-containing proteins (KBTBs), characterised by the core LIR sequence WVxV .
Polycystin domain (Polycystin_dom)
Type: Domain

This entry represents the polycystin domain from group II of Transient receptor potential (TRP) channels (TRPP) including PKD1, PKD2 and PKD2L. The polycystin domain displays a sandwich-like shape with five β-sheets in the tilted middle layer, three α-helices on one side, and a large loop with two short antiparallel β-sheets on the other .
Cysteine protease ATG4, F-type LIR motif (ATG4_LIR)
Type: Conserved_site

LC3 Interacting Regions (LIRs), also known as ATG8-interacting motifs (AIMs), are short-linear motifs (SLiMs) of autophagy receptors and adaptor proteins that facilitates the selective recruitment of autophagy substrates to the autophagosome. ATG8 proteins are highly conserved in eukaryotes and play a key role in selective autophagy as they recognise and bind different autophagy receptors and adaptors containing a specific class of SLiMs. LIRs are characterised by degenerated sequences with a four-residue core central sequence involved in ATG8-binding, with the W/Y/FxxL/I/V pattern. Based on the aromatic amino acid in position 1 they can be classified into W-type, Y-type and F-type. This entry represents the F-type LIR motif from cysteine protease ATG4, which contains the sequence FEI/VL. There are acidic residues at the N-terminal of this motif (Asp and Glu), which may contribute to stabilize the binding or may provide specificity toward a certain class of ATG8 proteins . This entry includes proteins from chordates.