SII-SWORD/CoKE huggingface dataset:
Csal_0991-like, N-terminal domain (Csal_0991-like_N)
Type: Domain

This entry represents a domain found at the N-terminal end of the probable membrane-anchored ferredoxin csal_0991 from Chromohalobacter salexigensis and similar sequences from proteobacteria. Csal_0991 participates in the electron transfer process during N,N-dimethylglycine (DMG) degradation to sarcosine . This domain was previously known as DUF3483. It is often found associated with

and

.
Cell division protein FtsA, C-terminal (FtsA_C)
Type: Domain

FtsA is essential for bacterial cell division, and co-localizes to the septal ring with FtsZ. It has been suggested that the interaction of FtsA-FtsZ has arisen through coevolution in different bacterial strains .

This C-terminal domain is found in FtsA from Firmicutes (Gram-positive bacteria). It acts as an intra-molecular switch, triggered by ATP, to promote polymerisation of the whole protein and to attach it to the membrane .
Bacteriophage Mu, Gp27 (Phage_Mu_Gp27)
Type: Family

This entry is represented by Bacteriophage Mu, Gp27. It is probably the small subunit of terminase, which recognises viral DNA, binds to the packaging initiation site (pac) and regulates the ATPase activity of the terminase large subunit . The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Retrograde transport protein Dsl1 N-terminal domain (Dsl1_N_dom)
Type: Domain

Dsl1 is a peripheral membrane protein, part of the DSL1 complex, required for transport between the Golgi and the endoplasmic reticulum . It is localised to the ER membrane, and bridges the other two subunits of the complex, Tip20 and Sec39. DSL1 complex, together with conserved oligomeric Golgi (COG), Golgi-associated retrograde protein (GARP), and the exocyst, is a member of the complexes associated with tethering containing helical rods (CATCHR) family, which are evolutionary related and share structural features . This complex interacts at its base with ER SNAREs and at its tip with COPI vesicles, thus, it captures Golgi-derived COP-I vesicles and facilitates their fusion with the ER the Dsl1 complex, upstream of SNARE complex formation . The C-terminal domain is involved in binding to the Sec39 subunit of the Dsl1p complex . The N-terminal complexes with another subunit of the Dsl1p complex called Tip20 which forms heterodimers by pairing the N termini of each protein .
Retrograde transport protein Dsl1, C-terminal domain (Dsl1_C)
Type: Domain

Dsl1 is a peripheral membrane protein part of the DSL1 complex, required for transport between the Golgi and the endoplasmic reticulum . It is localised to the ER membrane, and bridges the other two subunits of the complex, Tip20 and Sec39. DSL1 complex, together with conserved oligomeric Golgi (COG), Golgi-associated retrograde protein (GARP), and the exocyst, is a member of the complexes associated with tethering containing helical rods (CATCHR) family, which are evolutionary related and share structural features . This complex interacts at its base with ER SNAREs and at its tip with COPI vesicles, thus, it captures Golgi-derived COP-I vesicles and facilitates their fusion with the ER the Dsl1 complex, upstream of SNARE complex formation . The C-terminal domain is involved in binding to the Sec39 subunit of the Dsl1p complex . The N-terminal complexes with another subunit of the Dsl1p complex called Tip20 which forms heterodimers by pairing the N termini of each protein .
Protein of unknown function DUF3487 (DUF3487)
Type: Family

This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 121 to 136 amino acids in length. This protein has a conserved RLN sequence motif.
Protein-glutamine gamma-glutamyltransferase TgpA, N-terminal (TgpA_N)
Type: Domain

This domain can be found at the N terminus of TgpA from Pseudomonas aeruginosa. TgpA is a transglutaminase that plays a critical role in the viability of Pseudomonas aeruginosa . This domain is composed of 5 transmembrane helices .
VC2046 family (VC2046_fam)
Type: Family

This entry represents a group of family of uncharacterised proteins mainly found in gammaproteobacteria, including VC2046 from Vibrio cholerae (also known as QueD-like protein,

). They were annotated as ribosomal SSU S4 p proteins but there is not evidence supporting this, and it is, apparently, a missannotation. Proteins in this family are typically between 162 to 178 amino acids in length.
Protein of unknown function DUF3489 (DUF3489)
Type: Family

This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 84 to 211 amino acids in length. This protein has a single completely conserved residue W that may be functionally important.
NPK1-activating kinesin-like protein, C-terminal (NACK_C)
Type: Domain

This domain is found at the C terminus of plant kinesin-like proteins NACK1 and NACK2. NACK1 (NPK1-activating kinesin-like protein 1) is key regulator of plant cytokinesis . NACK2 (TETRASPORE) is required for male meiotic cytokinesis .
Protein of unknown function DUF3491 (DUF3491)
Type: Family

This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 286 to 3225 amino acids in length. This protein is found associated with

. This protein is found associated with

.
Protein LOW PSII ACCUMULATION 1-like (LPA1-like)
Type: Family

This entry includes Protein LOW PSII ACCUMULATION 1 (LPA1) from plants and some uncharacterised proteins from Cyanobacteria (blue-green algae). Arabidopsis LPA1 is a chaperone required for efficient photosystem II (PSII) assembly. It binds to psbA during de novo biogenesis of PSII .
Ice-binding protein (Ice-bd_prot)
Type: Family

This entry represents ice-binding proteins mainly found in bacteria and fungi. In Antarctic bacterium Flavobacterium frigoris PS1, FfIBP is an ice-binding protein (IBP) that inhibits ice growth through direct interaction with ice crystals to permit the survival of polar organisms in extremely cold environments . In arctic yeast Leucosporidium sp, LeIBP, an ice-binding protein, can lower the freezing point below the melting point once it binds to ice . The 3D structure of these proteins is a discontinuous β-solenoid with a triangular cross-section and an adjacent α-helix .
Domain of unknown function DUF3496 (DUF3496)
Type: Domain

This presumed domain is functionally uncharacterised. This domain is found in eukaryotes. This domain is about 110 amino acids in length.
MgsA AAA+ ATPase, C-terminal (MgsA_C)
Type: Domain

The MgsA protein possesses DNA-dependent ATPase and ssDNA annealing activities . MgsA contributes to the recovery of stalled replication forks and therefore prevents genomic instability caused by aberrant DNA replication . Additionally, MgsA may play a role in chromosomal segregation . This is consistent with a report that MgsA co-localises with the replisome and affects chromosome segregation . This domain represents the C-terminal region of MgsA. The structure of MgsA has been solved .

This domain is also found in the ATPase WRNIP1 which functions as a modulator of initiation or reinitiation events during DNA polymerase delta-mediated DNA synthesis .
Disabled homolog 2-interacting protein, C-terminal domain (DAB2P_C)
Type: Domain

This entry represents a domain found at the C terminus of some GTPase-activating proteins (also known as GAP) found in animals, including Disabled homologue 2-interacting protein (DAB2P) and Ras/Rap GTPase-activating protein SynGAP (SYGP1). DAB2P functions as a tumour suppressor that is also involved in several processes such as innate immune response and inflammation and plays a key role in brain development and function . SYGP1 is essential for postsynaptic signalling and has been related to brain injury, leading to long-term learning and memory deficits .

This domain, which is found associated with the RasGAP domain (

) and the C2 domain (

), includes a coiled-coil domain that forms a parallel trimer in solution .
Protein of unknown function DUF3499 (DUF3499)
Type: Family

This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 125 to 163 amino acids in length.
Protein of unknown function DUF3500 (DUF3500)
Type: Family

This family of proteins is functionally uncharacterised. This protein is found in bacteria and eukaryotes. Proteins in this family are typically between 335 to 438 amino acids in length. This protein has a conserved GHH sequence motif. This protein has two completely conserved G residues that may be functionally important.
Protein of unknown function DUF3501 (DUF3501)
Type: Family

This family of proteins is functionally uncharacterised. This protein is found in bacteria and archaea. Proteins in this family are about 200 amino acids in length. The structure of protein of unknown function (YP_111841.1) from B. pseudomallei has been solved.
Telomerase ribonucleoprotein complex - RNA-binding domain (Telomerase_RBD)
Type: Domain

Telomeres in most organisms are comprised of tandem simple sequence repeats . The total length of telomeric repeat sequence at each chromosome end is determined in a balance of sequence loss and sequence addition . One major influence on telomere length is the enzyme telomerase . It is a reverse transcriptase that adds these simple sequence repeats to chromosome ends by copying a template sequence within the RNA component of the enzyme . The RNA binding domain of telomerase - TRBD - is made up of twelve α helices and two short β sheets . How telomerase and associated regulatory factors physically interact and function with each other to maintain appropriate telomere length is poorly understood. It is known however that TRBD is involved in formation of the holoenzyme (which performs the telomere extension) in addition to recognition and binding of RNA .
RNA helicase NPH-II (NPH-II)
Type: Family

RNA helicase NPH-II or I8 is found in Poxviridae. It is essential for viral replication. Plays an important role during transcription of early mRNAs, presumably by preventing R-loop formation behind the elongating RNA polymerase. Acts as NTP-dependent helicase that catalyzes unidirectional unwinding of 3'tailed duplex RNAs. It might also play a role in the export of newly synthesized mRNA chains out of the core into the cytoplasm and is required for propagation of viral particles.
ZMYM2-like/QRICH1, C-terminal domain (ZMYM2-like_C)
Type: Domain

This entry (ex DUF3504) represents the C-terminal domain in Zinc finger MYM-type protein 2, 3, 4, QRICH1 and the uncharacterised KIAA1958 protein. This domain is functionally uncharacterised.

QRICH1 acts as a mediator of the integrated stress response through transcriptional control of protein homeostasis under conditions of ER stress .

Zinc finger MYM-type proteins 2, 3, and 4 (ZMYM2, ZMYM3, ZMYM4) are nuclear proteins involved in chromatin regulation, transcriptional repression, and DNA repair. ZMYM2 participates in retrotransposon silencing and DNA double-strand break repair by interacting with chromatin-modifying complexes and DNA-PK, and is targeted for degradation by cereblon-modulating drugs. ZMYM3 functions as a scaffold protein in gene silencing and DNA repair, facilitating BRCA1 recruitment to damaged chromatin through H2AX binding. ZMYM4 interacts with the transcription factor B-MYB, undergoes SUMOylation, and is essential for early cranial gene expression and craniofacial development. These proteins collectively highlight the importance of MYM-type zinc finger proteins in genome maintenance and developmental processes .
Bud3, N-terminal (Bud3_N)
Type: Domain

This domain is found in the N-terminal of the yeast Bud3 protein. Bud3 is involved in bud-site selection in budding yeasts. This domain has a conserved ENL sequence motif .
THAP9-like, helix-turn-helix domain (THAP9-like_HTH)
Type: Domain

This entry represents the DNA-binding helix-turn-helix domain (HTH) of human DNA transposase THAP9, which specifically recognises the bipartite 5'-TXXGGGX(A/T)-3' consensus motif and mediates transposition .
Cilia- and flagella-associated protein 206 (FAP206)
Type: Family

Proteins in this entry are found in eukaryotes. There are two conserved sequence motifs: GFC and GLL. This family is also known as UPF0704, whose members include FAP206, a protein associated with cilia and flagella. In the ciliate Tetrahymena, the cilium has radial spokes, each of which is a macromolecular complex essential for motility. A triplet of three radial spokes, RS1, RS2, and RS3, is repeated every 96 nm along the doublet microtubule. Each spoke has a distinct base that docks to the doublet and is linked to different inner dynein arms. Knockout of the FAP206 gene results in slow cell motility and the 96-nm repeats lack RS2 and dynein c. FAP206 is probably part of the front prong and docks RS2 and dynein c to the microtubule .
Protein of unknown function DUF3509 (DUF3509)
Type: Family

This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 92 to 110 amino acids in length. This protein has two completely conserved residues (G and R) that may be functionally important.
Protein of unknown function DUF3511 (DUF3511)
Type: Family

This presumed domain is functionally uncharacterised. This domain is found in eukaryotes. This domain is about 50 amino acids in length. This domain has two completely conserved residues (Y and K) that may be functionally important.
Protein of unknown function DUF3512 (DUF3512)
Type: Family

This presumed domain is functionally uncharacterised. This domain is found in eukaryotes. This domain is typically between 231 to 249 amino acids in length. This domain is found associated with

.
CAS family, C-terminal (CAS_C)
Type: Domain

This domain is found in the C terminus of the CAS family members.

The CAS (Crk-Associated Substrate) protein family is a group of scaffolding proteins that play important modulatory roles in both normal and pathological cell growth regulation. They contain an N-terminal Src homology 3 (SH3) domain and a substrate domain (SD). The SD contains a large number of YxxP motifs, which when phosphorylated by Src-family kinases provide canonical binding sites for proteins containing SH2 domains such as Crk, Crk-L, CRKII .
Protein of unknown function DUF3514 (DUF3514)
Type: Family

This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 368 to 823 amino acids in length.
Protein of unknown function DUF3515 (DUF3515)
Type: Family

This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 166 to 214 amino acids in length. This protein has a conserved RCG sequence motif.
Protein of unknown function DUF3516 (DUF3516)
Type: Family

This presumed domain is functionally uncharacterised. This domain is found in bacteria. This domain is typically between 460 to 473 amino acids in length. This domain is found associated with

,

.
Ubiquitin C-terminal hydrolase-like, DUF3517 (DUF3517)
Type: Domain

This domain is found at the C-terminal end of ubiquitin C-terminal hydrolases and similar sequences from eukaryotes. It is functionally uncharacterised, but it is found associated with

.

Deubiquitinating enzymes (DUBs) are capable of removing ubiquitin (Ub) from protein substrates and are involved in numerous biological processes . DUBs can be divided into 7 subfamilies: ubiquitin C-terminal hydrolase (UCH) , ubiquitin-specific processing protease (UBP or USP) , otubain protease (OUT), Machado-Joseph disease protease (MJD), JAB1/MPN/Mov34 metalloenzyme (JAMM) , monocyte chemotactic protein-induced protein (MCPIP) and the motif interacting with Ub-containing novel DUB family (MINDY) .
SWI/SNF-like complex subunit BAF250/Osa (BAF250/Osa)
Type: Family

This entry represents the mammalian BAF250a/b and its homologue osa from fruit flies . They are part of the SWI/SNF-like ATP-dependent chromatin remodelling complex that regulates gene expression through regulating nucleosome remodelling. In humans there are two BAF250 isoforms, BAF250a/ARID1a and BAF250b/ARID1b. BAF250a/b may be E3 ubiquitin ligases that target histone H2B .

This entry also includes Arabidopsis LFR protein, which is involved in leaf and flower development and is required for the formation of anther cell layers and normal expression of genes that regulates anther development .
Protein of unknown function DUF3519 (DUF3519)
Type: Family

This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 117 to 1154 amino acids in length. This protein has a single completely conserved residue Q that may be functionally important.
Uncharacterized protein YfbK, C-terminal (YfbK_C)
Type: Domain

This presumed domain is found in bacteria. This domain is about 180 amino acids in length, its function is unclear. This domain is found at the C-terminal of

.
NGX6/PGAP6/MYMK (NGX6/PGAP6/MYMK)
Type: Family

Proteins in this family include PGAP6 (also known as TMEM8A), NGX6 (also known as TMEM8B) and myomaker (also known as TMEM8C). TMEM8C is embedded in the plasma membrane with seven membrane-spanning regions and a required intracellular C-terminal tail. It is essential for myoblast fusion and sufficient to promote fusion of fibroblasts with muscle cells . TMEM8A and TMEM8B has no fusogenic activity. TMEM8A is a GPI-specific phospholipase A2 involved in Nodal signaling modulation through CRIPTO shedding . TMEM8B plays a role in cell adhesion modulation in nasopharyngeal carcinoma cells .
ATPase family AAA domain-containing protein 3, N-terminal (ATAD3_N)
Type: Domain

This is the conserved N-terminal domain of ATPase family AAA domain-containing protein 3 (ATAD3) which is involved in dimerisation and interacts with the inner surface of the outer mitochondrial membrane . This domain is found associated with the AAA ATPase domain

. ATAD3 is essential for mitochondrial network organisation, mitochondrial metabolism and cell growth at organism and cellular level. It may also play an important role in mitochondrial protein synthesis.
Protein of unknown function DUF3525 (DUF3525)
Type: Family

This family of proteins is functionally uncharacterised. This protein is found in viruses. Proteins in this family are about 360 amino acids in length.
Protein of unknown function DUF3526 (DUF3526)
Type: Family

This presumed domain is functionally uncharacterised. This domain is found in bacteria. This domain is typically between 149 to 170 amino acids in length. This domain has a single completely conserved residue P that may be functionally important.
Transcriptional factor DELLA, N-terminal (TF_DELLA_N)
Type: Domain

Gibberellins are plant hormones which have great impact on growth signalling. DELLA proteins are transcriptional regulators of growth related proteins that lack a DNA binding domain and exert its negative regulation of gibberellin responses through interaction with other transcription factors . DELLAs are downregulated when gibberellins bind to their receptor GID1 , which forms a complex with DELLA proteins and signals them towards 26S proteasome. The N-terminal of DELLA proteins contains conserved DELLA and TVHYNP motifs which are important for GID1 binding and proteolysis of the DELLA proteins .
Tubuliform egg casing silk strands structural domain (RP1-2)
Type: Domain

Spiders use fibroins to make silk strands. This family includes tubuliform silk fibroins which are used to protect egg cases. This domain is a structural domain which is found in repeats of up to 20 in many individuals (although this is not necessarily the case). RP1 makes up structural domains in the N-terminal while RP2 makes up structural domains in the C-terminal .
Protein of unknown function DUF3527 (DUF3527)
Type: Family

This presumed domain is functionally uncharacterised. This domain is found in eukaryotes. This domain is about 120 amino acids in length. This domain has a conserved CDCGGWD sequence motif.
Uncharacterised protein family, zinc metallopeptidase-like (Unchr_Zn-peptidase-like)
Type: Family

This family of proteins is functionally uncharacterised. However, it does contain an HEXXH motif characteristic of metallopeptidases. This protein is found in bacteria and eukaryotes. Proteins in this family are typically between 625 to 773 amino acids in length.
Domain of unknown function DUF3528, homeobox protein, eukaryotic (DUF3528)
Type: Domain

This domain of unknown function is found at the N terminus of some Homeobox proteins belonging to the ABD-B family. It is found in association with

.
Cofactor assembly of complex C subunit B, CCB1 (CCB1)
Type: Family

Cofactor maturation pathways such as the CCB system (system IV) for cytochrome c-heme attachment are conserved in all organisms performing oxygenic photosynthesis . The CCB system consists of four proteins: CCB1-4. The four CCBs are well conserved between green algae and plants . This entry represents CBB1.
Protein of unknown function DUF3531 (DUF3531)
Type: Family

This family of proteins is functionally uncharacterised. This protein is found in bacteria and eukaryotes. Proteins in this family are typically between 149 to 199 amino acids in length.
Par3/HAL, N-terminal (Par3/HAL_N)
Type: Domain

This domain is found in eukaryotes and is about 150 amino acids in length. It has a conserved GILD sequence motif. Some proteins containing this domain are essential for cell polarity establishment and maintenance such as Par3 (partitioning defective), and some are involved in conversion of histidine into ammonia (a crucial step for forming histamine in humans) such as Histidine ammonia lyase (HAL). This N-terminal domain is found to mediate oligomerization critical for the membrane localization of Par-3. It is also found to possess a self-association capacity via a front-to-back mode in Par-3 and HAL proteins. However, unlike the Par-3 N-terminal domain which self-assembles into a left-handed helical filament, the HAL N-terminal domain does not tend to form a helical filament but rather self-assembles into circular oligomeric particles. This has been suggested to be likely due to the absence of equivalent charged residues that are essential for the longitudinal packing of the Par-3 N-terminal domain filament .
Protein of unknown function DUF3536 (DUF3536)
Type: Family

This presumed domain is functionally uncharacterised. This domain is found in bacteria and archaea. This domain is typically between 274 to 285 amino acids in length. This domain is found associated with

.
Protein of unknown function DUF3537 (DUF3537)
Type: Family

This family of transmembrane proteins are functionally uncharacterised. This protein is found in eukaryotes. Proteins in this family are typically between 427 to 453 amino acids in length.
Large proline-rich protein BAG6 (BAG6)
Type: Domain

This domain is found in large proline-rich protein BAG6 protein. It has a conserved SDL sequence motif.
PII-interacting protein X, cyanobacteria (PipX)
Type: Family

This protein family is predominantly found in cyanobacteria and includes PII-interacting protein X (PipX) from Synechococcus elongatus. PipX modulates the expression of genes involved in nitrogen assimilation by interacting with the global nitrogen transcription factor NtcA and the signal transduction protein PII. It is involved in several regulatory pathways . The crystal structure of this protein shows a tudor-like domain (TLD), formed by a highly bent β-sheet that mediates the interactions with both PII and NtcA, and two C-terminal helices .
Protein of unknown function DUF3540 (DUF3540)
Type: Family

This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 212 to 238 amino acids in length. This protein has a conserved SCL sequence motif.
Protein of unknown function DUF3541 (DUF3541)
Type: Family

This entry represents a group of uncharacterised proteins mainly found in proteobacteria.