SII-SWORD/CoKE huggingface dataset:
Large ribosomal subunit protein bL9m, C-terminal domain (Ribosomal_bL9m_C)
Type: Domain

This entry represents a presumed domain found at the C-terminal of the large ribosomal subunit protein bL9m (mitochondrial) from animals. This domain may adopt a similar fold to that of prokaryotic large ribosomal subunit protein bL9.

Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites . About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits.

Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome .
Type III effector protein HopBA1 (HopBA1)
Type: Family

HopBA1 is a type III effector protein that triggers an RBA1-dependent cell-death response. It folds into an α/β structure that consists of a central mixed β-sheet packed on both sides with α-helices . HopBA1 is structurally similar to proteins members of EreA/ChaN-like superfamily. It contains a ψ-loop between strands 5 and 6.
Dark, CARD domain (Dark_CARD)
Type: Domain

This entry represents a caspase recruitment domain (CARD) present in a set of Dark (Drosophila Apaf-1-related killer) proteins from insects, including Apaf-1/CED-4-related caspase activator Dapaf-1S from Drosophila melanogaster (Dark). Dark protein is part of the apoptosome complex and plays a key role in procaspases activation and apoptosis . This N-terminal CARD in Dark belongs to the α-helical Death domain superfamily (

) and interacts with the N-terminal CARD of Dronc protein .
SwaI restriction endonuclease (SwaI)
Type: Family

SwaI is a Type IIP restriction endonuclease that recognises a palindromic eight base pair symmetric sequence, 5'-ATTTAAAT-3', and cleaves this target sequence at its centre to generate blunt-ended DNA fragments. SwaI forms a dimeric α/β structure, with each subunit having a central cradle-like mixed β-sheet with two helices packed on its concave side and a C-terminal helix contributing to the dimer interface . SwaI has a significant similarity to other restriction endonucleases such as HincII, NlaIV, HindIII and EcoRV.
2-thiouridine synthetase TtuA-like, N-terminal LIM domain (TtuA-like_LIM_N)
Type: Domain

TtuA is an oxygen-labile iron-sulfur protein that is involved in a post-transcriptional thiolation of RNA. The iron-sulfur cluster of TtuA is required for sulfurtransferase activity. The enzyme structure consists of three domains: a central catalytic domain and two Zn-fingers . This entry represents the N-terminal Zn-finger domain that share a significant similarity to LIM domains.

This domain is also found in tRNA 2-thiolation protein NcsA required for formation of thiolated tRNA(Lys)UUU as well as in the cytoplasmic tRNA 2-thiolation protein 1 that plays a central role in 2-thiolation of mcm5S2U at tRNA wobble positions of tRNA(Lys), tRNA(Glu) and tRNA(Gln).
DNA endonuclease I-HmuI-like, NUMOD-like domain (I-HmuI_NUMOD-like)
Type: Domain

This entry represents the C-terminal NUMOD1-like DNA-binding HTH domain present in a set of intron-encoded endonucleases (homing endonucleases) such as I-HmuI from Bacteriophage SP01 and similar proteins .
Ufm1-specific protease, MPN domain (UfSP_MPN)
Type: Domain

UfSP is a cysteine protease that activates Ufm1 from its precursor by processing the C-terminal to expose the conserved Gly necessary for substrate conjugation and de-conjugates Ufm1 from the substrate. UfSP from C. elegans consists of three domains: MPN domain, N-domain and a catalytic domain. This entry represents the MPN domain that forms an α/β globular structure with a central mixed β-sheet packed on both sides with helices and a pair of two strands and a helix. This domain modulates both substrate recognition and deufmylation activity .
Nitric oxide reductase subunit B, cytochrome c-like domain (NorB_cytochrome_c-like)
Type: Domain

This domain is found in Nitric oxide reductase subunit B from Pseudomonas aeruginosa (NorB) and similar bacterial sequences. NorB is the large component of the anaerobic respiratory chain that transforms nitrate to dinitrogen (denitrification). This entry represents the cytochrome C-like domain of NorB, which has 12 α-helices in the transmembrane region with two heme irons and one non-heme iron .
CT0912-like, C-terminal domain (CT0912-like_C)
Type: Domain

This domain is found at the C-terminal end of

from Chlorobaculum tepidum (CT0912), a functionally uncharacterised protein with a ferredoxin-like domain repeat. This domain shows an α-β configuration.
LPG0439, HIT-related (LPG0439_HIT-like)
Type: Domain

These are uncharacterised proteins that are related to proteins which are members of the HIT-like superfamily.
DIP2116-like, N-terminal domain (DIP2116-like_N)
Type: Domain

This domain is found at the N-terminal of the putative membrane anchored protein DIP2116 from Corynebacterium diphtheriae (

). It shows an immunoglobulin-like fold.
Gins51, C-terminal domain (Gins51_C)
Type: Domain

This domain is found at the C-terminal of the DNA replication complex GINS family protein TK0536 from Thermococcus kodakarensis (Gins51,

). Gins51 is composed of a large α-helical domain at the N-terminal, and a small β-stranded domain at the C-terminal. This mobile C-terminal domain acts as a hook to bind the archaeal GINS-associated nuclease to form the 'CGM' unwindosome complex. It shows an α-β configuration .
T26-6p, immunoglobulin-like domain 1 (T26-6p_Ig-like_dom_1)
Type: Domain

This domain is found at the N-terminal in T26-6p from Thermococcus and similar archaeal sequences. T26-6p has three domains: two β- sandwich with two sheets made of four antiparallel β-strands (this entry and

) and a bundle of five α-helices (

) .
T26-6p, second immunoglobulin-like domain (T26-6p_Ig-like_dom_2)
Type: Domain

This domain is found in T26-6p from Thermococcus and similar archaeal sequences. T26-6p has three domains: two β- sandwich with two sheets made of four antiparallel β-strands (

and this entry) and a bundle of five α-helices (

) .
CED4, winged-helix domain (CED4_WHD)
Type: Domain

This entry represents a winged-helix-like domain (WHD) found at the C-terminal of CED4 and similar proteins from nematodes. CDE4 together with EGL1, CED9, and CED3, forms a crucial component of the apoptotic signaling cascade necessary for triggering programmed cell death during both embryonic and postembryonic development . Molecular dynamics studies indicate that this WH domain may regulate CED4 dissociation from CED9 .
BT_3535-like (BT_3535-like)
Type: Family

This family represents the functionally uncharacterised protein BT_3535 from Bacteroides thetaiotaomicron (

) and similar sequences found in bacteroidetes. This protein is organised into two domains.
PspC-related, ToastRack domain (PspC-rel_ToastRack)
Type: Domain

This entry represents the ToastRack domain found at the C-terminal end of a group of proteins related to PspC predominantly found in firmicutes. This domain is often associated to

.
PspC-related, transmembrane region (PspC-rel_TM)
Type: Domain

This entry represents the transmembrane region found in a group of proteins related to PspC predominantly found in firmicutes. This domain is often associated to

.
Flagellar calcium-binding protein, EF-hand domain (FCABP_EF-hand)
Type: Domain

This entry represents a EF-hand domain found in Flagellar calcium-binding protein from Trypanosoma cruzi (FCABP) and similar sequences mainly found in lower eukaryotes. This protein contains two EF-hand domains, the first of which is represented by this entry. FCABP may contribute to the rapid motility of the trypanosomes, playing a role either in flagellar structure or in calcium metabolism. It is targeted to the flagella where it regulates flagellar function and assembly .
Sperm microtubule inner protein 1, C-terminal (SPMIP1_C)
Type: Domain

This entry represents the C-terminal region of human Sperm microtubule inner protein 1 (SPMIP1). SPMIP1 is a microtubule inner protein (MIP) part of the doublet microtubules (DMTs) in the sperm axoneme . It binds to protofilament B09 along with CFAP90 in the sperm DMTs.
McpB, first HAMP domain (McpB_HAMP_1st)
Type: Domain

This entry represents the first of five HAMP domains of Methyl-accepting chemotaxis protein McpB from Pseudomonas aeruginosa and similar sequences mainly from gammaproteobacteria. McpB, also known as Aerotaxis transducer Aer2, is a chemoreceptor that plays a critical role in the virulence and pathogenesis of the bacteria in a variety of hosts. This domain consists of a monomeric unit of two parallel α-helices joined by an elongated connector of 12-14 residues. The three N-terminal are likely to be required for dimerisation .
VtrA, C-terminal periplasmic domain (VtrA_C)
Type: Domain

VtrA forms a complex with VtrC on the surface of the membrane that surrounds the bacterial cell. These two proteins create a platform that can bind to bile salts and trigger the release of bacterial toxins. This entry represents the C-terminal periplasmic domain of VtrA from Vibrio parahaemolyticus (

), which interacts with the VtrC periplasmic domain. The VtrA periplasmic domain adopts an α/β structure consisting of a five-stranded antiparallel β-sheet and two helices packed on one side of it . Members of this group are specific to Vibrionales.
Homoserine dehydrogenase, C-terminal domain (HSD_C)
Type: Domain

Homoserine dehydrogenase (HSD) coordinates a critical branch point of the metabolic pathway that leads to the synthesis of bacterial cell-wall components such as L-lysine and m-DAP in addition to other amino acids such as L-threonine, L-methionine and L-isoleucine. The enzyme structure consists of three domains. This entry represents the C-terminal domain of staphylococcal homoserine dehydrogenases, which folds into a four-stranded antiparallel β-sheet with two α-helices packed on one side .
Histidine kinase-like, sensor domain (His-kinase-like_sensor)
Type: Domain

This entry represents a sensor domain found in a group of predicted histidine kinases and diguanylate cyclases mainly from proteobacteria, including

from Shewanella oneidensis. It folds into an α/β structure consisting of a curved β-sheet and an α-helix packed on the concave side of it .
SseL-like, C-terminal domain (SseL-like_C)
Type: Domain

This entry represents the C-terminal catalytic domain from a group of CE proteases from human pathogens including SseL from Salmonella typhimurium , which are dedicated deubiquitinases (DUBs), proteases that reverse the addition of ubiquitin to substrates, and effectively hijacks the host's ubiquitination processes .
ElaD/SseL-like, N-terminal domain (ElaD/SseL-like_N)
Type: Domain

This entry represents the N-terminal helical domain found in a group of CE proteases from human pathogens, including ElaD from E.coli and SseL from Salmonella typhimurium , which are dedicated deubiquitinases (DUBs), proteases that reverse the addition of ubiquitin to substrates, and effectively hijacks the host's ubiquitination processes . This domain is structurally similar to VHS domains and it serves to localise the catalytic domain (

) through an additional Ub binding site .
Pch2-like, N-terminal domain (Pch2-like_N)
Type: Domain

Pch2/TRIP13 belongs to a family of proteins known as AAA-ATPases and via an adaptor protein binds to the closed form of MAD2. Pch2/TRIP13 then unfolds a part of the MAD2 protein, converting MAD2 into the open form. The C.elegans ortholog Pch2 forms a stable hexamer and its structure consists of a N-terminal domain and a AAA-ATPase module composed of two subdomains. This entry represents the N-terminal domain that consists of a four-stranded β-sheet and an α-helix packed on it. The structure of this domain (

) shows a clear relationship to the N-terminal substrate recognition domains of a AAA+ classic remodeller sub-family that includes NSF, p97, and PEX1 .
LiaF, transmembrane domain (LiaF_TM)
Type: Domain

This entry represents the transmembrane region (TM) found at the N-terminal of LiaF (

), which is thought to be a sensory domain. It may tie into a two-component system to regulate the membrane integrity and permeability in response to the stress signal.
Transcription factor IIB, C-terminal module 2 (TFIIB_C_2)
Type: Domain

In the pathogenic trypanosome, Trypanosoma brucei, transcription factor IIB (tTFIIB) is essential for spliced leader (SL) RNA gene transcription and cell viability, but has a highly divergent primary sequence in comparison to TFIIB in other eukaryotes. Structure analysis of the C-terminal region of trypanosome TFIIB, reveals 2, closely packed helical modules followed by a C-terminal extension of 32 aa. The trypanosome-specific region comprises the second helical module and the C-terminal extension. Both helical modules contain the canonical 5-helix cyclin fold characteristic of TFIIB proteins . This domain is mostly found in Trypanosomatidae. The first helical module is represented in

.
ARP associated Restriction Endonuclease (REase-ARP-assoc)
Type: Family

This entry represents a rapidly evolving Restriction Endonuclease (REase) family of bacterial proteins observed in host systems and predicted to counter the action of viral ribosylating toxins, associated with ARG and Rhodanese-Phosphatase domain (ARP). It potentially functions as an effector in these systems .
Decaheme cytochrome c component MtrC/MtrF, domain I (MtrC-MtrF_dom_I)
Type: Domain

This entry represents the domain I (N-terminal) of the decaheme cytochrome c component MtrC from the MtrCAB complex and its homologue MtrF, which is part of the MtrFDE complex. In Shewanella oneidensis, these proteins are at bacterial cell surface at the termini of trans-outer-membrane electron transfer conduits and allow the utilisation of extracellular mineral forms of iron and manganese as respiratory electron acceptors . MtrC/MtrF consist of four domains: domain I and III containing seven antiparallel β-strands in an extended Greek key topology; domains II and IV (

) each bind five tightly packed hemes covalently attached to the Cys residues of the five CXXCH motifs in each domain and form the central core (

), flanked by domains I and III (

) .
Dual OB-containing domain (DuOB_dom)
Type: Domain

This entry represents a region found in a group of prokaryotic proteins that contains two domain copies of the OB fold. There is nearly absolutely conserved cysteine, serine/threonine, arginine, and aspartate residues which are predicted to line a deep cleft formed at the interface of the two OB domains. The predicted spatial arrangement of the tandem OB domains closely parallels OB-dyads from single-stranded nucleic acid-end binding proteins, such as the telomere-binding domain alpha-subunit, with the nucleic acid being lodged in a cleft formed by the two OB domains. Drawing an analogy to the SRAP domain, it has been suggested that the DuOB domain could potentially form cross links to DNA at the abasic sites via its conserved cysteine. It is found on the genome adjacent to

and

, which could potentially also catalyse thiotransfer reactions required for forming or resolving the cysteine-DNA crosslinks, paralleling recent findings where HD phosphatases mediate the transfer of a phosphorylated substrate to a hydroxyl-group-containing residue .
OmcA-like, N-terminal domain (OmcA-like_N)
Type: Domain

This entry represents the N-terminal domain of OmcA (

) from Shewanella oneidensis and similar proteins. OmcA is a decaheme c-type cytochrome homologue of MtrF and MtrC . OmcA may be able to receive electrons from the MtrCAB or MtrFDE complexes through the interaction with MtrC or MtrF . OmcA, MtrF and MtrC are involved in the use of manganese and iron as terminal electron acceptors.
Outer membrane cytochrome MtrC/MtrF-like, domains II/IV (Mtrc-MtrF_dom_II/IV)
Type: Domain

This entry represents domains II and IV found in decaheme cytochrome c component MtrC from the MtrCAB complex and its homologues MtrF (which is part of the MtrFDE complex) and OmcA. In Shewanella oneidensis, these proteins are located at the bacterial cell surface at the termini of trans-outer-membrane electron transfer conduits and allow the utilization of extracellular mineral forms of iron and manganese as respiratory electron acceptors . MtrC/MtrF/OmcA consist of four domains: domain I and III contain seven antiparallel beta-strands in an extended Greek key topology; domains II and IV each bind five tightly packed hemes covalently attached to the Cys residues of the five CXXCH motifs in each domain and form the central core, flanked by domains I (

) and III (

) .
Peptidoglycan muramidase Tse3, catalytic domain (Tse3_cat)
Type: Domain

This entry represents the catalytic domain found in Peptidoglycan muramidase Tse3. Tse3 is a toxin secreted by the H1 type VI (H1-T6SS) secretion system into the periplasm of recipient cells. This protein degrades peptidoglycan via muramidase activity. Tse3 is composed of a small N-terminal domain (

) and a C-terminal catalytic domain, which contains two major lobes that form an open, accessible catalytic groove with three calcium-binding ions .
GMT-like, wHTH domain (GMT_wHTH)
Type: Domain

This entry represents a rapidly-evolving wHTH domain C-terminally fused to Rossmann fold methylase specifically related to the guanine methylase (GMT). Often co-occurs on the genome across a broad range of bacterial phylogenies with a further gene encoding a RADICAL SAM enzyme (

). This two-gene island is predicted to catalyse a DNA/RNA guanine modification comparable to the precursors of Wybutosine. This wHTH domain could be a sensor that recognises a rapidly-evolving nucleic acid sequence, implicating the gene pair in a conflict response to an invasive genic element .
GNAT-like, C-terminal domain, phage-lihe (GNAT-like_C_phage-like)
Type: Domain

This domain is found at the C-terminal of a group of proteins from tailed bacteriophages and bacterial prophages, including some predicted GNAT family N-acetyltransferase. It has been characterised as part of a nucleic acid modifying system in certain phages. This system may modify tRNAs that are encoded adjacent to the system on the genome .
GNAT-like, N-terminal domain (GNAT-like_N)
Type: Domain

This domain is found at the N-terminal of a group of proteins from tailed bacteriophages and bacterial prophages, including some predicted GNAT family N-acetyltransferase. It has been characterised as part of a nucleic acid modifying system in certain phages. This system may modify tRNAs that are encoded adjacent to the system on the genome .
TY-Chap, C-terminal domain (TY-Chap_C)
Type: Domain

This entry represents a domain found at the C-terminal end of a group of T3SS (YopN, CesT) and YbjN peptide-binding chaperone 1 (TY-Chap) proteins from actinomycetes. Members are observed in host systems and predicted to counteract the action of viral ribosylating toxins. It is found C-terminal to the N-terminal (

) and central (

) domains .
TY-Chap, central domain (TY-Chap_M)
Type: Domain

This entry represents a domain found centrally located in a group of T3SS (YopN, CesT) and YbjN peptide-binding chaperone 1 (TY-Chap) proteins from bacteria. Members are observed in host systems and predicted to counteract the action of viral ribosylating toxins. It is found between the TY-Chap N-terminal (

) and C-terminal (

) domains .
TY-Chap, N-terminal domain (TY-Chap_N)
Type: Domain

This entry represents a domain found at the N-terminal end of a group of T3SS (YopN, CesT) and YbjN peptide-binding chaperone 1 (TY-Chap) proteins from bacteria. Members are observed in host systems and predicted to counteract the action of viral ribosylating toxins. It is found N-terminal to the central (

) and C-terminal (

) domains .
Molecular chaperone Tir-like (Tir-like)
Type: Family

This entry represents a group of hypothetical bacterial proteins. Many members are annotated as molecular chaperone Tir, a novel member of the CesT/Tir superfamily of chaperones found linked to the YjfJ family of PspA genes.
ARG and Rhodanese-Phosphatase-superfamily-associated domain 2 (ARPP-2)
Type: Domain

ARPP-2 (ARG and Rhodanese-Phosphatase-superfamily-associated Protein domain 2) shows a distinguishing group of absolutely conserved residues distinct from ARPP-1 (

). ARPP-2 is typically found fused to a C-terminal HTH domain and adjacent to a Rot/TROVE domain fused to a vWA domain .
TOTE conflict system, primase domain (TOTE_primase)
Type: Domain

This entry represents the presumed primase domain predicted to function as RNA polymerase in the TOTE (TPR, OB, TBP, Effector) conflict systems, potentially generating transcripts for hybrid duplex formation .
Protein M, C-terminal (M_C)
Type: Domain

This domain is found in proteins from Mycoplasmaceae, including Uncharacterized protein MG281 from Mycoplasma genitalium, also known as protein M. This virulence protein consists of two domains and N- and C-terminal fragments. This entry represents the C-terminal region, which is probably disordered .
Protein M, smaller domain (M_smaller_dom)
Type: Domain

This domain is found in proteins from Mycoplasmaceae, including Uncharacterized protein MG281 from Mycoplasma genitalium, also known as protein M. This virulence protein consists of two domains. The larger one (

) binds the IgG light chain to block the binding of antibody to antigen and includes a leucine-rich repeat (LRR)-like subdomain. This domain folds into two α-helices .
PurT/PurK-like, preATP-grasp domain (PurT/PurK_preATP-grasp)
Type: Domain

This domain precedes the ATP-grasp domain in a number of ribonucleotide synthetases, such as PurT, PurK and Pur6
.

PurT is involved in the de novo purine biosynthesis. PurK, N5-carboxyaminoimidazole ribonucleotide (N5_CAIR) synthetase, catalyses the conversion of 5-aminoimidazole ribonucleotide (AIR), ATP, and bicarbonate to N5-CAIR, ADP, and Pi.