SII-SWORD/CoKE huggingface dataset:
Type 2A encapsulin shell protein SrpI-like (SrpI-like)
Type: Domain

This entry includes type 2A encapsulin shell protein SrpI from Synechococcus elongatus and its homologues from Mycobacteria, such as

from M. leprae, which has been described as the most antigenic protein in human leprosy patients and useful for serodiagnosis of leprosy . SrpI forms a nanocompartment that is probably involved in sulfur metabolism .

Some members of this entry contain an N-terminal cyclic nucleotide binding domain. This entry also includes proteins annotated as phage capsid proteins, such as

, suggesting that in bacteria this protein is a co-opted phage protein. There is a clear evolutionary relationship between the bacterial encapsulins and Caudovirales bacteriophages as they share the HK97 fold of the capsid proteins.
Protein of unknown function DUF6406 (DUF6406)
Type: Family

This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001916) is described by MIBiG as an example of the polyketide biosynthetic class, in particular the lavendiol biosynthetic gene cluster from Streptomyces lavendulae .
Protein of unknown function DUF6405 (DUF6405)
Type: Family

This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000434) is described by MIBiG as an example of the NRP (non-ribosomal peptide) biosynthetic class, in particular the SW-163C biosynthetic gene cluster from Streptomyces sp. SNA15896 .
Protein of unknown function DUF6404 (DUF6404)
Type: Family

This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001055) is described by MIBiG as an example of the NRP (non-ribosomal peptide) and polyketide biosynthetic classes, in particular the yersiniabactin biosynthetic gene cluster from Escherichia coli [[cite17049458]]. This family appears to be predominantly found in Proteobacteria.
Protein of unknown function DUF6403 (DUF6403)
Type: Family

This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001447) is described by MIBiG as an example of the polyketide biosynthetic class, in particular the primycin biosynthetic gene cluster from Saccharomonospora azurea SZMC 14600 .
Protein of unknown function DUF6402 (DUF6402)
Type: Family

This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000464) is described by MIBiG as an example of the NRP (non-ribosomal peptide) biosynthetic class, in particular the xenoamicin A biosynthetic gene cluster from Xenorhabdus doucetiae . This family appears to be predominantly found in proteobacteria.
Protein of unknown function DUF6401 (DUF6401)
Type: Family

This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001580) is described by MIBiG as an example of the polyketide biosynthetic class, in particular the ebelactone biosynthetic gene cluster from Kitasatospora aburaviensis . This family appears to be predominantly found in Actinobacteria.
CRISPR-associated protein Cas6-like, N-terminal domain (CRISPR-assoc_Cas6-like_N)
Type: Domain

This entry represents the N-terminal domain of the CRISPR-associated protein Cas6 found in bacteria, predominantly in cyanobacteria and chloroflexi and some firmicutes species.

Cas6 is a member of the RAMP (repeat-associated mysterious protein) superfamily . It is among the most widely distributed Cas proteins and is found in both bacteria and archaea . Cas6 functions in the generation of CRISPR-derived guide RNAs for invader defense in prokaryotes . The structure of this protein showed it adopts a tandem ferredoxin/RRM fold .

The CRISPR-Cas system is a prokaryotic defence mechanism against foreign genetic elements. The key elements of this defence system are the Cas proteins and the CRISPR RNA.
Protein of unknown function DUF6400 (DUF6400)
Type: Family

This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000144) is described by MIBiG as an example of the following biosynthetic class, polyketide, in particular the salinomycin biosynthetic gene cluster from Streptomyces albus . This family appears to be predominantly found in Actinobacteria.
Protein of unknown function DUF6399 (DUF6399)
Type: Family

This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000967) is described by MIBiG as an example of the following biosynthetic classes, NRP (non-ribosomal peptide) and polyketide, in particular the calyculin A biosynthetic gene cluster from uncultured Candidatus Entotheonella sp. . This family appears to be predominantly found in proteobacteria and cyanobacteria.
Domain of unknown function DUF6398 (DUF6398)
Type: Domain

This domain is functionally uncharacterised, it is present in proteins from bacteria and archaea. This domain is approximately 100 amino acids in length and contains a conserved WA sequence motif.
Protein of unknown function DUF6397 (DUF6397)
Type: Family

This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000406) is described by MIBiG as an example of the following biosynthetic class, NRP (non-ribosomal peptide), in particular the phosphinothricintripeptide biosynthetic gene cluster from Streptomyces viridochromogenes . This family appears to be predominantly found in Actinobacteria.
Domain of unknown function DUF6396 (DUF6396)
Type: Domain

This presumed domain of unknown function is found in uncharacterised proteins mainly from Proteobacteria, and is about 100 amino acids in length. It has the conserved sequences RxxRY and PLPPAxLPxWDG.
Protein of unknown function DUF6395 (DUF6395)
Type: Family

This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000755) is described by MIBiG as an example of the following biosynthetic class, saccharide. .
Protein of unknown function DUF6394 (DUF6394)
Type: Family

This family of proteins found in bacteria is functionally uncharacterised.
Protein of unknown function DUF6393 (DUF6393)
Type: Family

This entry represents a member of a biosynthetic gene cluster (BGC) from Proteobacteria. This BGC (BGC0000385) is described by MIBiG as an example of the following biosynthetic class, NRP (non-ribosomal peptide), in particular the lysobactin biosynthetic gene cluster from Lysobacter sp. ATCC 53042 .
Protein of unknown function DUF6392 (DUF6392)
Type: Family

This family of proteins is functionally uncharacterised and it is predominantly found in Gammaproteobacteria. Proteins in this family are typically between 55 and 170 amino acids in length. Proteins in this family are likely to be related to pyocin immunity protein.
FRAS1-related extracellular matrix protein, N-terminal domain (FRAS1-rel_N)
Type: Domain

This entry represents a domain found at the N terminus of FRAS1-related extracellular matrix proteins (also known as Frem related proteins) predominantly in chordates. In humans, the FRAS1-related extracellular matrix protein 1 was reported to be essential for the normal adhesion of the embryonic epidermis . FRAS1-related extracellular matrix protein 2 is involved in the development of eyelids and the anterior segment of the eyeballs and has been related to cryptophthalmos (a rare congenital disorder characterised by ocular dysplasia with eyelid malformation) .
LPS-assembly protein LptD, central domain (LptD_2)
Type: Domain

This domain is localized to the central region of a set of LPS (lipopolysaccharide)-assembly protein LptD that likely represents the LptD homologue of Bacteroidetes.

LptD forms a complex with LptE, which is involved in the assembly of LPS in the outer leaflet of the outer membrane. It determines N-hexane tolerance and is involved in outer membrane permeability as well as being ssential for envelope biogenesis .
Protein of unknown function DUF6390 (DUF6390)
Type: Family

This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001065) is described by MIBiG as an example of the following biosynthetic class, polyketide, in particular the herboxidiene biosynthetic gene cluster from Streptomyces chromofuscus . This family appears to be predominantly found in Actinobacteria.
Protein of unknown function DUF6389 (DUF6389)
Type: Family

This entry represents a member of a bacterial biosynthetic gene cluster (BGC). This BGC (BGC0000081) is described by MIBiG as an example of the following biosynthetic class, polyketide, in particular the kedarcidin biosynthetic gene cluster from Streptoalloteichus sp. ATCC 53650 .
Protein of unknown function DUF6388 (DUF6388)
Type: Family

This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001859) is described by MIBiG as an example of the following biosynthetic class, other (unspecified), in particular fosfomycin biosynthetic gene cluster from Pseudomonas syringae . This family is predominantly found in Proteobacteria. Some members are putative DNA repair proteins.
Origin recognition complex subunit 3, insertion domain (ORC3_ins)
Type: Domain

This is the insertion domain of ORC subunit 3 (ORC3) predominantly found in chodates, arthropodes and vertebrates, located between the N-terminal AAA+-like subunit and the C-terminal winged-helix (WH) DNA-binding domain . ORC3 is a component of the origin recognition complex (ORC) that binds origins of replication, required to assemble the pre-replication complex necessary to initiate DNA replication. This insertion domain forms a bi-lobed α-helical protuberance that engages a short α-helix formed at the ORC6 C-terminal, allowing its binding to ORC1-5 subunits , which constitute the ORC core .
Protein of unknown function DUF6387 (DUF6387)
Type: Family

This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001055) is described by MIBiG as an example of the following biosynthetic classes, NRP (non-ribosomal peptide) and polyketide, in particular the yersiniabactin biosynthetic gene cluster from Escherichia coli . This family appears to be predominantly found in Proteobacteria.
Protein of unknown function DUF6386 (DUF6386)
Type: Family

This entry represents a member of a bacterial biosynthetic gene cluster (BGC). This BGC (BGC0001796) is described by MIBiG as an example of the following biosynthetic class, NRP (non-ribosomal peptide), in particular the tauramamide biosynthetic gene cluster from Brevibacillus laterosporus DSM 25 .
Oligopeptidase A, N-terminal domain (OpdA_N)
Type: Domain

This entry represents the N-terminal domain of Oligopeptidase A (OpdA,

), which belongs to the M3A family of peptide-degrading metalloproteases. This enzyme may play a specific role in the degradation of signal peptides after they are released from precursor forms of secreted proteins . In Arabidopsis, it localizes both to mitochondria and chloroplasts .
Origin recognition complex subunit 3, N-terminal (ORC3_N)
Type: Domain

This entry represents the N-terminal domain (approximately 300 residues) of subunit 3 of the eukaryotic origin recognition complex (ORC). Origin recognition complex (ORC) is composed of six subunits that are essential for cell viability. They collectively bind to the autonomously replicating sequence (ARS) in a sequence-specific manner and lead to the chromatin loading of other replication factors that are essential for initiation of DNA replication . This domain is predicted to contain an AAA fold but lack the residues important for ATP hydrolysis, thus, it is called AAA+-like .
FHF complex subunit HOOK-interacting protein, KELAA motif (FHIP_KELAA_motif)
Type: Conserved_site

This short motif is found at the C terminus of the FHF complex subunit HOOK-interacting protein (also known as FTS and Hook-interacting protein, FHIP). This complex may function to promote vesicle trafficking and/or fusion via the homotypic vesicular protein sorting complex (the HOPS complex) . The motif has a conserved KELAA sequence for which it is named. Members of this entry are predominantly found in animals.
FHF complex subunit HOOK-interacting protein, C-terminal (FHIP_C)
Type: Domain

This entry represents a short presumed domain located close at the C terminus of the FHF complex subunit HOOK-interacting protein (also known as FTS and Hook-interacting protein, FHIP). The FHF complex may function to promote vesicle trafficking and/or fusion via its interaction with the homotypic vesicular protein sorting complex (the HOPS complex) . The function of this domain is still unknown.
Domain of unknown function DUF5916 (DUF5916)
Type: Domain

This entry represents an uncharacterised domain found mostly in bacterial proteins. In CBM9 domain containing proteins, this domain is C-terminal to the CBM9 domain. According to BOCTOPUS prediction this region has a membrane barrel topology, which suggests that proteins containing this domain maybe novel carbohydrate channels.
Nitrogen regulation protein NtrY-like, N-terminal domain (NtrY-like_N)
Type: Domain

This entry represents the probable sensor region of the two component regulator protein NtrY, predominantly found in proteobacteria . This region includes four probable transmembrane helices.
Mesaconyl-CoA hydratase, archaea (MC_hydratase_acr)
Type: Family

This entry includes Mesaconyl-CoA hydratase from archaea, which is involved in the methylaspartate cycle. It catalyses the reversible hydration of mesaconyl-CoA to yield beta-methylmalyl-CoA (

) .
Phenol-soluble modulin delta protein (PSM_delta)
Type: Family

This entry represents the phenol-soluble modulin delta peptide found in staphylococcal species .
Protein of unknown function DUF6196 (DUF6196)
Type: Family

This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001381) is described by MIBiG as an example of the polyketide biosynthetic class. It includes a member from the brasilinolide A biosynthetic gene cluster from Nocardia terpenica . This family is found in bacteria.
Protein of unknown function DUF6195 (DUF6195)
Type: Family

This entry represents a member of a biosynthetic gene cluster (BGC) from the bacterial family Streptomycetaceae. This BGC (BGC0000703) is described by MIBiG as an example of the saccharide biosynthetic class. It includes a member from the kanamycin biosynthetic gene cluster from Streptomyces kanamyceticus .
Domain of unknown function DUF6194 (DUF6194)
Type: Domain

This entry represents a domain found in members of a biosynthetic gene cluster (BGC). This BGC (BGC0001597) is described by MIBiG as an example of the polyketide biosynthetic class. It includes a member from the fluvirucin B2 biosynthetic gene cluster from Actinomadura fulva subsp. indica . Members of this group are predominantly found in bacteria. This domain is predicted to adopt an α-β configuration.
Protein of unknown function DUF6197 (DUF6197)
Type: Family

This entry represents a group of uncharacterised proteins from tailed bacteriophagues and actinobacteria, including a member of a biosynthetic gene cluster (BGC) from the bacterial family Streptomycetaceae. This BGC (BGC0000703) is described by MIBiG as an example of the saccharide biosynthetic class. It includes a member from the kanamycin biosynthetic gene cluster from Streptomyces kanamyceticus .
Protein of unknown function DUF6198 (DUF6198)
Type: Family

This family represents a putative integral membrane protein that is likely to be the membrane component of an ABC transport system. This family is found in bacteria and archaea.
Protein of unknown function DUF6199 (DUF6199)
Type: Family

This entry represents a member of a biosynthetic gene cluster (BGC) from Streptomycetales. This BGC (BGC0000087) is described by MIBiG as an example of the polyketide biosynthetic class. It includes a member from the lasalocid biosynthetic gene cluster from Streptomyces lasaliensis (also known as Streptomyces lasalocidi) .
Protein of unknown function DUF6200 (DUF6200)
Type: Family

This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001943) is described by MIBiG as an example of the NRP (non-ribosomal peptide) biosynthetic class. It includes a member from the vioprolides A biosynthetic gene cluster from Cystobacter sp. . This family is found in bacteria.
Protein of unknown function DUF6201 (DUF6201)
Type: Family

This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001133) is described by MIBiG as an example of the NRP (non-ribosomal peptide) biosynthetic class. It includes a member from the taxlllaid A biosynthetic gene cluster from Xenorhabdus bovienii SS-2004 . This family is found in Proteobacteria.
Protein of unknown function DUF6193 (DUF6193)
Type: Family

This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000087) is described by MIBiG as an example of the polyketide biosynthetic class. It includes a member from the lasalocid biosynthetic gene cluster from Streptomyces lasaliensis . This family appears to be predominantly found in Actinobacteria.
Protein of unknown function DUF6192 (DUF6192)
Type: Family

This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000713) is described by MIBiG as an example of the saccharide biosynthetic class. It includes a member from from the ribostamycin biosynthetic gene cluster from Streptomyces ribosidificus . This family is mainly found in Streptomycetales.
Protein of unknown function DUF6191 (DUF6191)
Type: Family

This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0002014) is described by MIBiG as an example of the polyketide and NRP (non-ribosomal peptide) biosynthetic classes. It includes a member of the pepticinnamin E biosynthetic gene cluster from Actinobacteria bacterium OK006 . This family is found in Actinobacteria.
Protein of unknown function DUF6190 (DUF6190)
Type: Family

This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0002018) is described by MIBiG as an example of an unspecified biosynthetic class. It includes a member from the azomycin biosynthetic gene cluster from Streptomyces cattleya NRRL 8057 = DSM 46488. This family appears to be predominantly found in bacteria.
Protein of unknown function DUF6189 (DUF6189)
Type: Family

This entry represents a member of a bacterial biosynthetic gene cluster (BGC). This BGC (BGC0000807) is described by MIBiG as an example of the saccharide biosynthetic class. It includes a member of the phosphonoglycans biosynthetic gene cluster from Stackebrandtia nassauensis DSM 44728 .
GPI ethanolamine phosphate transferase 2, C-terminal (PIGG/GPI7_C)
Type: Domain

This entry corresponds to the C-terminal transmembrane region of the GPI ethanolamine phosphate transferase 2 (PIGG/GPI7). These proteins are involved in the pathway glycosylphosphatidylinositol-anchor biosynthesis . In humans, this enzyme has been related to disorders leading to including intellectual disability (ID), seizures, and facial dysmorphism . In yeast it is known as las21, and it is essential for cell separation .
Ets1, N-terminal flanking region of Ets domain (Ets1_N_flank)
Type: Domain

Ets1 is a member of the Ets family of transcription factors in which the DNA-binding activity is in an autoinhibited state. The autoinhibition of Ets1 is mediated by structural coupling of the regions flanking the Ets domain. The inhibitory regions are folded as helices HI1 and HI2 N-terminal to the ETS domain and as H4 C-terminal to the ETS domain, which are packed together to form an inhibitory module .

This domain represents the N-terminal flanking region of Ets domain which contains the residues forming HI1 and HI2 helices and additional residues (244-301) N-terminal to HI1. HI1 and HI2 exert the autoinhibitory function by directing the inhibitory residues N-terminal to HI1 to mask the Ets domain DNA-binding surface. These residues are flexible and function by masking the DNA-binding surface of the Ets domain. Phosphorylation of serine residues present in this region enhances autoinhibition dramatically. These inhibitory sequences are required for cooperative DNA binding . Members of this entry are found among chordates.
S-layer protein Slr4 (Slr4)
Type: Family

This family represents a novel S-layer protein widely distributed in Gammaproteobacteria including species of Pseudoalteromonas and Vibrio, and are found exclusively in marine metagenomes. These proteins assemble into paracrystalline sheets with a unique square lattice symmetry .
Protein of unknown function DUF6055 (DUF6055)
Type: Family

This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and fungi.
Protein of unknown function DUF6056 (DUF6056)
Type: Family

This family of integral membrane proteins is functionally uncharacterised. This family of proteins is found in bacteria, archaea and viruses. There is a conserved NYL sequence motif.
Protein of unknown function DUF6057 (DUF6057)
Type: Family

This family of integral membrane proteins is functionally uncharacterised. This family of proteins is found primarily in Bacteroidetes bacteria.
NAD(P)H-quinone oxidoreductase subunit 2, N-terminal (Ndh2_N)
Type: Domain

This domain represents the N-terminal domain of NAD(P)H-quinone oxidoreductase subunit 2 (or subunit B, NdhB), part of the P-module (pumping) of the photosynthetic complex I mostly from plants and cyanobacteria, which is structurally and functionally related to the respiratory complex I from mitochondria and bacteria. NdhB is involved in the electron transfer between photosynthetic complex I and photosystem I .
Protein of unknown function DUF6058 (DUF6058)
Type: Family

This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001590) is described by MIBiG as an example of the following biosynthetic class, polyketide. This family includes a protein from the formicamycins A-M biosynthetic gene cluster from Streptomyces sp. KY5 .
Transmembrane protein 131-like, second Ig-like domain (TMEM131-like_Ig_dom2)
Type: Domain

This entry represents the second Ig-like domain in TMEM131L and third in TMEM131.

Transmembrane protein 131-like (TMEM131L) was identified as a negative regulator of thymocyte proliferation that acts through mixed Wnt-dependent and independent mechanisms. It has two isoforms, L and S, which have different subcellular localisation. L isoform, the membrane-associated form, inhibits canonical Wnt/beta-catenin signalling through the induction of lysosome-dependent degradation of the active phosphorylated form of the LRP6 coreceptor. This protein was firstly described as containing three conserved homology domains (CHD1, 2 and 3), a transmembrane region and a C-terminal serine-rich region . Using structure prediction models from AlphaFold, it has been possible to identify the CHDs as Ig-like domains.

TMEM131 is a collagen binding transmembrane protein involved in collagen secretion by recruiting the ER-to-Golgi transport complex TRAPPIII . Human TMEM131 is predicted to contain eight Ig-like domains.
RING finger protein 37, N-terminal (Ubox5_N)
Type: Domain

This entry represents the N-terminal domain of the RING finger protein 37 (RNF37), an U-box domain-containing protein. This is a variable region that probably has a role in function regulation .
Domain of unknown function DUF5919 (DUF5919)
Type: Domain

This entry represents the C-terminal domain of proteins containing the SAV2148-like HEPN domain mostly found in the bacterial class Actinomycetia. The function of this domain is unknown.