SII-SWORD/CoKE huggingface dataset:
Plant cysteine-rich protein domain (CR_prot_dom_plant)
Type: Domain

This domain is found in a group of plant cysteine-rich proteins, including cysteine-rich receptor-like protein kinases 6/8/10 and cysteine-rich repeat secretory protein 1 from Arabidopsis thaliana . This domain is usually found C-terminal to two copies of

. It is predicted to adopt an α-helical structure.
S-layer protein, spectrin-like repeat (SbsA_spectrin-like)
Type: Domain

This entry represents a Spectrin-like domain present in the bacterial S-layer protein from Geobacillus stearothermophilus (SbsA, ) and similar sequences from bacillales. This domain shows structural similarity to the Spectrin domain (

).
NADH:ubiquinone reductase, helical insertion domain (NDH2_hel_ins)
Type: Domain

This entry represent the helical insertion domain of NDH2, a NADH-ubiquinone oxidoreductase from Plasmodium falciparum , an interesting target for antimalarial drug development. This domain seems to be specific to sequences from Apicomplexa.
Listeria nuclear targeted protein A, helical domain (LntA_helical)
Type: Domain

This entry represents the C-terminal helical domain present in LntA protein, a virulence factor from Listeria monocytogenes . LntA targets and inhibits the chromatin repressor BAHD1 in the host cell nucleus to activate interferon-stimulated genes. LntA interacts directly with a central domain of BAHD1 via a surface patch of conserved positive charges, located nearby a groove on the elbow region of LntA . This group of proteins is specific to Listeria species.
Tyrosine--tRNA ligase SYY-like, C-terminal domain (SYY-like_C)
Type: Domain

This entry represents the C-terminal domain of Tyrosine--tRNA ligases which contains the S4 motif that binds RNA . Members of this group are mainly found in bacteria, including tyrS from Escherichia coli which structure has been determined (

). TyrS catalyses the attachment of L-tyrosine to tRNA(Tyr) in a two-step reaction: tyrosine is first activated by ATP to form Tyr-AMP and then transferred to the acceptor end of tRNA(Tyr) .
Transcriptional regulatory protein PF0864-like, C-terminal domain (PF0864-like_C)
Type: Domain

This entry represents the C-terminal domain of the Transcriptional Regulatory Protein PF0864 from Pyrococcus furiosus and similar prokaryotic proteins. PF0864 is 162 amino acids long and contains an N-terminal HTH asnC-type domain responsible for DNA binding. The crystal structure of PF0864 (

) reveals a dimeric α-β barrel structure of this region which is related to

. The function and specific role of PF0864 in transcriptional regulation remains unknown.
NACHT N-terminal helical domain (NNH)
Type: Domain

This entry represents an helical domain found at the N-terminal of a group of proteins from NACHT conflict systems (named NHH for NACHT N-terminal helical) mainly found in cyanobacteria, including

from Rivularia sp. PCC 7116 . This position is frequently occupied by an effector domain.
NACHT C-terminal Alpha/Beta domain (NCAB)
Type: Domain

This domain, which contains α-helices and β-strands, is found at the C-terminal of a group of cyanobacterial sequences from NACHT conflict systems .
Phage capsid-like, C-terminal (Phage_capsid-like_C)
Type: Domain

This entry represents a domain found in bacteria and viruses (Caudovirales), including bacteriophage capsid proteins. The major capsid protein of Enterobacteria phage HK97 assembles to form an icosahedral capsid . Included within the capsid protein is the delta domain which acts as the scaffold upon which the capsid is built . Bacterial and archaeal encapsulin-like systems and HK97-type viruses share a common ancestor and it is likely that encapsulins have evolved from HK97-type phages

]. This domain is found at the C-terminal in some instances, associated with a protease domain at the N-terminal.
Prohead serine protease domain (Peptidase_S78_dom)
Type: Domain

This entry represents the protease domain found in Caudovirus prohead serine proteases and in a number of bacteria possibly as the result of horizontal transfer.
DIP0205-like, N-terminal domain (DIP0205-like_N)
Type: Domain

This domain is found at the N-terminal end of DIP0205 from Corynebacterium diphtheriae (

) and other putative phage capsid proteins from tailed bacteriophages and bacterial prophages. This domain adopts an α-helical structure. It is often found associated to

.
Symporter small accessory protein (Symport_access)
Type: Family

Members of this family share a conserved N-terminal region of about 33 amino acids, with variable length C-terminal regions. As the conserved region is highly hydrophobic, and member proteins are nearly always encoded adjacent to sodium:solute symporter family proteins, typically with coding regions that overlap by at least one nucleotide, it seems likely that members of this family act as a transporter small subunit or assembly factor. Note that because members of this family may be shorter than 40 amino acids, members of this family may have been missed systematically by many annotation pipeline versions. Members of this family are found in both archaea and bacteria.
Heme A synthase, rhodobacterales (HemA_synt_rhodobact)
Type: Family

This family represents a small group of heme A synthases (CtaA) from Rhodobacterales. CtaA catalyses the conversion of haem O to haem A by two successive hydroxylations of the methyl group at C8. The first hydroxylation forms haem I, the second hydroxylation results in an unstable dihydroxymethyl group, which spontaneously dehydrates, resulting in the formyl group of haem A .
Flavin-dependent monooxygenase, oxygenase subunit HsaA (HsaA)
Type: Family

This entry represents Flavin-dependent monooxygenase, oxygenase subunit HsaA and related proteins mainly found in Actinomycetes. HsaA catalyses the o-hydroxylation of 3-hydroxy-9,10-secoandrosta-1,3,5(10)-triene-9,17-dione to 3,4-dihydroxy-9,10-secoandrosta-1,3,5(10)-triene-9,17-dione in the catabolism of cholesterol .
Fructokinase (ScrK)
Type: Family

This entry represents fructokinase ScrK from Lactobacillales, whose amino acid sequence has no significant similarity to fructokinase genes from Klebsiella pneumoniae or Vibrio alginolyticus .
Npun_R2821-like (Npun_R2821-like)
Type: Family

This entry represents a protein family from Cyanobacteria, including the predicted Sugar transferase Npun_R2821	from Nostoc punctiforme (

). Members of this entry are almost perfectly matched to the presence of the cyanoexosortase CrtB (

).
Carboxyl-terminal processing protease CtpA (Cterm_S41_CtpA)
Type: Family

This entry represents a family of proteins from Cyanobacteria, including carboxyl-terminal processing protease A from Synechocystis sp. (CtpA), which processes the photosystem II core complex protein D1 (PsbA) .
DVU0150-like (DVU0150-like)
Type: Family

This family includes a group of poorly characterised sequences mainly from Thermodesulfobacteriota, such as DVU0150 (

) from Desulfovibrio vulgaris . Its function is not yet clear but it has been suggested to be involved syntrophic metabolism between D. vulgaris and M. barkeri. .
HAH_0734-like (HAH_0734-like)
Type: Family

This uncharacterised protein family is found in halophilic archaea, such as HAH_0734 (

) from Haloarcula hispanica. It has several conserved motifs WHGP, QLWC and RxYxP. Members of this entry average about 87 amino acids in length and are predicted to adopt a predominantly β-structure with a short α-helix.
GDSL lipase Rv0518 (GDSL_Rv0518)
Type: Family

This family represents a group of GDSL lipases from Mycobacteriaceae, including Rv0518 from Mycobacterium tuberculosis. Rv0518 catalyses the hydrolysis of p-nitrophenyl (pNP) esters, being pNP-decanoate (C10) the preferred substrate. It can also use pNP-octanoate (C8), pNP-dodecanoate (C12) and pNP-tetradecanoate (C14). It has lower activity with pNP-butyrate (C4), pNP-palmitate (C16) and pNP-stearate (C18) [[cite31125644]]. It does not have phospholipase A1 activity . Rv0518 might help bacteria to utilize available lipids for its growth as well as provide resistance to various intracellular stresses by cell wall modulation resulting in enhanced intracellular survival .
Carboxyl-terminal processing protease CtpB (Cterm_S41_CtpB)
Type: Family

This entry represents a family of proteins from Cyanobacteria, including carboxyl-terminal protease CtpB from Synechocystis sp. (

), a paralogue of CtpA (

) whose exact function has not been yet clarified .
Carboxyl-terminal processing protease CtpC (Cterm_S41_CtpC)
Type: Family

This entry represents a family of proteins from Cyanobacteria, including carboxyl-terminal protease CtpC from Synechocystis sp. (slr1751,

), a paralogue of CtpA (

) that may act in crucial housekeeping processes directly linking with survival . Its exact function has not been yet clarified .
Carboxyl-terminal processing protease CtpZ (Cterm_S41_CtpZ)
Type: Family

This entry represents a family of serine endopeptidases from cyanobacteria that belong to a subgroup distinct from its paralogues in the families of the carboxyl-terminal processing proteases CtpA, CtpB, and CtpC (

,

and

). Members are predominantly found in various species of Synechococcus and Prochlorococcus. While CtpA processes the photosystem II core complex protein D1 (PsbA), and CtpC is essential and may have a general housekeeping role , the specific function of this protein is unknown.
Bilirubin reductase, N-terminal domain (BilR_N)
Type: Domain

This entry includes bilirubin reductase from Clostridioides difficile (BilR), as found in the gut microbiome, and similar sequences mainly found in firmicutes. While BilR fom Clostridioides difficile is a monodomain protein, some members of this entry are longer and this constitutes the N-terminal domain, such as in BilR form Mediterraneibacter gnavus.

Bilirubin, a haem breakdown product excreted in bile into the human gut, is converted to urobilinogen by gut bacteria, in a process protective against jaundice from bilirubin reabsorption. This process is catalysed by BilR . Urobilinogen oxidizes to urobilin, which gives urine its yellow colour.
HTH-type transcriptional regulator BilQ (BilQ)
Type: Family

This entry represents a family of proteins from firmicutes, including HTH-type transcriptional regulator BilQ from Clostridioides difficile. BilQ regulates expression of the bilirubin reductase operon (including bilQ, bilR and bilS) .
Glycerol facilitator-aquaporin gla (Gla)
Type: Family

This family includes Glycerol facilitator-aquaporin gla, a mixed channel protein that transports both water and glycerol . Members are specific to Lactobacillales.
Aroma-sacti cluster domain (Aroma_sacti_dom)
Type: Domain

The aroma-sacti cluster domain appears to be found exclusively in biosynthetic gene clusters (BGC) that include both a radical SAM/SPASM domain peptide maturase and RiPP precursor peptide. In some cases, the domain occurs in the N-terminal region of RiPP precursors with known sulfur-to-alpha-carbon (sacti) bonds formed between a Cys and a Gly residue (sequences included in

). Other members of the family (e.g.

) lack the critical Cys residues, but instead have an aromatic C-terminal residue, either Phe or Trp. Strangely, however, some members of the family have long N-terminal extensions with domain content suggesting MFS transporter activity.
Flavodoxin-like domain-containing protein BilS (BilS)
Type: Family

This entry represents flavodoxin-like domain-containing protein BilS from Clostridioides difficile and similar sequences primarily in Gram-positive bacteria of the gut microbiome. BilS is a flavodoxin-like protein, regularly found in operons with the bilirubin reductase BilR and the MarR family transcriptional regulator BilQ. Together with BilR, BilS catalyses the reduction of mesobilirubin and/or bilirubin to urobilinogen, a key step during haem degradation. It is probably involved in electron transfer .
Type III secretion system effector HrpZ (T3SS_HrpZ)
Type: Family

This family represents Harpin HrpZ from Pseudomonas sp. and similar sequences specific to Pseudomonas species. Harpins are proteins able to elicit hypersensitive response (HR) in non-host plants and are required for pathogenicity in host plants. HrpZ forms ion-conducting pores permeable for cations. Such pore-forming activity may allow nutrient release and/or delivery of virulence factors during bacterial colonization of host plants .
PA1571-like (PA1571-like)
Type: Family

This entry represents a group of small proteins from gammaproteobacteria, including PA1571 of Pseudomonas aeruginosa (

), which is homologous to BAL062_00718 from Acinetobacter baumannii, identified by transposon mutagenesis as a likely mediator of reduced sensitivity to colistin .
Cytochrome oxidase putative small subunit CydP (CydP)
Type: Family

This entry represents a group of small proteins with a highly hydrophobic core region from proteobacteria, including the cytochrome oxidase putative small subunit CydP . Members are found in the context of larger subunits of cytochrome bd oxidases, therefore, they are presumed to be a small subunit or assembly factor.
Asr1405/Asl0597-like (Asr1405_Asl0597-like)
Type: Family

This family appears to be restricted to nitrogen-fixing cyanobacteria. Asr1405 from Nostoc sp. (

) was shown to be induced by nitrogen limitation, while its paralogue Asl0597 (

) was not .
Npun_F0813-like (Npun_F0813-like)
Type: Family

Members of this family, including Npun_F0813 from Nostoc punctiforme (

), are uncharacterised proteins found in cyanobacteria that grow with a filamentous morphology .
Npun_F5560-like (Npun_F5560-like)
Type: Family

Members of this family, including Npun_F5560 (

) from Nostoc punctiforme PCC 73102, appear only in the cyanobacteria, and appear restricted to the subset of cyanobacteria that grow in elongated fibers and form heterocysts for nitrogen fixation. This entry describes full-length homologues of Npun_F5560, and currently excludes proteins lacking the N-terminal region, as from several species of Synechococcus.
Sfum_1244-like (Sfum_1244-like)
Type: Family

Members of this protein family, named for founding member Sfum_1244 (

) from the selenoprotein-rich species Syntrophobacter fumaroxidans, are uncharacterised proteins that occur primarily in Pseudomonadota and Thermodesulfobacteriota. The function of these proteins is unknown.
Glutaryl-CoA dehydrogenase ACD (GlutCoADH_Des)
Type: Family

This family includes glutaryl-CoA dehydrogenase ACD from Desulfococcus multivorans, which catalyses the dehydrogenation of Glutaryl-CoA to glutaconyl-CoA .
O-aminophenol oxidase PhsA (AmiPhnlOxPhsA)
Type: Family

This family includes O-aminophenol oxidase PhsA from Streptomyces antibioticus and similar sequences from actinomycetes. It may be involved in the spore pigmentation and melanin production. It catalyses the oxidative coupling of 2-aminophenols to form the 2-aminophenoxazinone chromophore. 2-aminophenoxazinone synthesis proceeds via a sequence of three consecutive 2-electron aminophenol oxidations .
Thiopeptide maturation pyridine synthase TbtD/PbtD (TbtD_PbtD_pyrid)
Type: Family

This family represents pyridine synthase synthases for thiopeptide (thiazolyl peptide) maturation, including TbtD in thiomuracin biosynthesis and PbtD (

) in GE2270A biosynthesis , which resemble the elimination domain (C-terminal domain) of class I lanthipeptide dehydratases, but those dehydratases convert Ser and Thr residues to dehydroamino acids. Members of this group are mainly found in actinomycetes.
Exosortase-dependent surface domain XDD4 (Xrt_dep_XDD4)
Type: Domain

This entry represents XDD4 (exosortase-dependent surface domain 4), the fourth in a series of domains or full-length proteins that appear always, or nearly always, to have a C-terminal sorting signal such as PEP-CTERM (

) that is recognized and processed by XrtA or another exosortase.
Heparin/heparin-sulfate lyase HepB (HepB)
Type: Family

This family represents heparin and heparin-sulfate lyase (HepB, also known as heparinase II), which cleaves both heparin and heparan sulfate glycosaminoglycans through a beta-elimination mechanism. It cleaves heparin at alpha-D-GlcNp2S6S(1->4) alpha-L-IdoAp2S and heparan sulfate at alpha-D-GlcNp2Ac(or 2S)6OH(1->4)beta-D-GlcAp . HepC specifically cleaves heparan sulfate-rich regions of acidic polysaccharides, it does not act on N,O-desulfated glucosamine or N-acetyl-O-sulfated glucosamine linkages. HepC functions in cleaving metazoan heparan sulfate and providing carbon, nitrogen and sulfate sources for microorganisms . The structure of Heparinase II has been solved .
Heparin-sulfate lyase HepC (HepC)
Type: Family

This family represents heparin-sulfate lyase (HepC, also known as heparinase III), which specifically cleaves heparan sulfate-rich regions of acidic polysaccharides, it does not act on N,O-desulfated glucosamine or N-acetyl-O-sulfated glucosamine linkages. HepC functions in cleaving metazoan heparan sulfate and providing carbon, nitrogen and sulfate sources for microorganisms .
Gamma-glutamyl-CDP-amidate hydrolase (GCDPHdlase)
Type: Family

This family includes gamma-glutamyl-CDP-amidate hydrolase (GCDPH) from Campylobacter jejuni and similar sequences from campylobacterales. GCDPH is involved in the biosynthesis of the O-methyl phosphoramidate (MeOPN) group found on the capsular polysaccharide (CPS) of C.jejuni . It catalyses the hydrolysis of CDP-L-glutamine to L-glutamate and cytidine diphosphoramidate .
TudS-related putative desulfidase (TudS-rel)
Type: Family

Members of this family of prokaryotic proteins typically show weak sequence similarity to

, the 2-thiouracil desulfurase (TudS) family. Proteins in this group frequently co-occur with the selenide, water dikinase SelD and with the [Fe8-S9] double-cubane cluster family

, plus frequent occurrence in a tandem gene pair with the putative ECF transporter S component proteins of

. These observations suggest both a role in the import and utilisation of some organic compound for anaerobic fermentation and a connection to anaerobic sulfur and/or selenium metabolism.
Npun_R2479-like (Npun_R2479-like)
Type: Family

This family includes Npun_R2479 (

) from Nostoc punctiforme and similar sequences found primarily in the group of Cyanobacteria that also contain Cyanoexosortase B (CrtB). Members show the HDIG motif of HD domain proteins .
Photosystem II high light acclimation Slr0320-like (Slr0320-like)
Type: Family

This entry represents a family of cyanobacterial proteins that contain the radical SAM domain (

), including Slr0320 from Synechocystis sp. (

), which is crucial for the functioning of photosystem II upon exposure to high light .
Npun_F0494-like (Npun_F0494-like)
Type: Family

This entry represents a group of uncharacterised proteins from cyanobacteria, including Npun_F0494 from Nostoc punctiforme (

). Most members are found encoded next to CobQ (

). The central motif LRREVDGQGxxxxxRLTPLG is highly conserved.
Type IV pilus, essential for biofilm suppression A-like (T4P_EbsA-like)
Type: Family

This entry represents a family of proteins from cyanobacteria, including EbsA (essential for biofilm self-suppression A) from Synechococcus elongatus (

), a protein that plays a role in both type IV pilus formation and protein secretion across the outer membrane, two processes that rely on the same set of genes .
Exosortase-associated protein EpsI, B-type, predicted (EpsI_type_B_pred)
Type: Family

This entry represents a family of proteobacterial proteins that contain the domain

.
Exosortase-associated protein EpsI, V-type, predicted (EpsI_type_V_pred)
Type: Family

This entry represents a family of proteobacterial proteins that contain the domain

. This variant form of EpsI occurs with the type V exosortase, XrtV, involved in sorting a subclass of PEP-CTERM proteins to the cell surface .
Sorting system accessory protein XrtV-like (XrtV-like)
Type: Family

Members of this hydrophobic protein family are found associated with the protein-sorting cysteine endopeptidase XrtV (exosortase V as in Victor), and likely participate in the proper targeting and localisation of client PEP-CTERM proteins. The system is mainly seen in Sphingomonadales.
DVU_1557-like (DVU_1557-like)
Type: Family

This family of putative redox proteins includes DVU_1557 (

) from Desulfovibrio vulgaris, as well as the related paralogues from Clostridium ljungdahlii. Members of this family are found in an extended conserved gene neighborhood that also includes a molybdopterin-dependent aldehyde oxidoreductase and the radical SAM (seleno)protein TrsS. The presence in Clostridium ljungdahlii, a species apparently without heme biosynthesis, has implications for the electron transfer pathways to which the proteins of the conserved gene neighborhood contribute .
Putative T6SS immunity periplasmic lipoprotein (T6SS_periplasmic_put)
Type: Family

Members of this family, including SARI_02726 (

) from Salmonella enterica subsp. arizonae and EC042_4532 (

) from sequence type ST31 strains of enteroaggregative Escherichia coli, are associated with type VI secretion systems (T6SS), and suggested to be immunity proteins with periplasmic localization. A well-conserved lipoprotein-type signal peptide and two widely separated well-conserved or invariant Cys residues support an extracytoplasmic location. .
Extracytoplasmic lipoprotein (Extrcyto_LP)
Type: Family

Members of this family are found primarily in the genus Acinetobacter. These proteins have four widely spaced invariant Cys residues, suggesting an extracytoplasmic (surface or periplasmic) location. About half the members of this family have an apparent lipoprotein signal peptide.
J517_1871 lipoprotein-like (J517_1871_lipoprot)
Type: Family

This entry represents a group of proteins commonly found in Acinetobacter and Acinetobacter phages, which are predicted lipoproteins. Many members contain a lipid attachment site and are predicted to show an extensive β-sheet structure.
Cation efflux protein, CzcI-like (CzcI-like)
Type: Family

This entry represents a family of proteins mainly found in Acinetobacter species. Members are metal resistance efflux proteins, related to the cobalt-zinc-cadmium transporter protein CzcI .
Scytonemin biosynthesis sensor histidine kinase Npun_F1277-like (Npun_F1277-like)
Type: Family

This entry represents a family of cyanobacterial sequences, including the histidine kinase Npun_F1277 from Nostoc punctiforme (

), part of a two-component regulatory system encoded upstream of the scytonemin gene cluster .
PT dipeptide repeat lipoprotein (Lipo_PTPT)
Type: Family

This entry represents a group of uncharacterised proteins specific to Acinetobacter. Members of this group show an N-terminal lipoprotein signal peptide, followed by a variable length stretch of Pro-Thr dipeptide repeats or a related Pro-rich region and the non-repetitive domain.
Filament integrity protein FraC (FraC)
Type: Family

This entry represents the Filament integrity protein FraC and related proteins found in cyanobacteria. FraC, along with FraD and SepJ (FraG), is found at intercellular septa in heterocyst-forming filamentous cyanobacteria such as Nostoc punctiforme. This protein is involved in filament integrity and is required for the integrity of cell junctions in general .
Alr0857-like (Alr0857-like)
Type: Family

This entry includes uncharacterised proteins, including Alr0857 protein (

) from Nostoc sp., that are found predominantly in cyanobacteria .
ZirU-like domain (ZirU-like_dom)
Type: Domain

This entry represents a domain that covers the whole protein length in ZirU from Salmonella, which shares with ZirS the property of requiring ZirT for its type Vb-like secretion and is homologous to immunoglobulin superfamily members . It is also found at the C-terminal end of several uncharacterised proteins. Members of this group are specific to enterobacterales.