SII-SWORD/CoKE huggingface dataset:
YjzC-like protein (YjzC)
Type: Family

The YjzC-like protein family includes the B. subtilis YjzC protein

, which is functionally uncharacterised.
YycC-like protein (YycC)
Type: Family

The YycC-like protein family includes the B. subtilis YycC protein

, which is functionally uncharacterised. There is a conserved HIL sequence motif that may be important for function.
Immunity protein WapI/YxiJ-like (WapI/YxiJ-like)
Type: Family

This is a family of immunity proteins, mainly from Bacillus spp, such as WapI. The immunity protein WapI specifically neutralizes its cognate toxin WapA to protect wapA+ cells from autoinhibition. WapA carries a C-terminal toxin domain (WapA-CT) that inhibits the growth of neighbouring cells .
YkyB-like protein (YkyB)
Type: Family

The YkyB-like protein family includes the B. subtilis YkyB protein

, which is functionally uncharacterised. Proteins in this family are approximately 150 amino acids in length and contain two conserved sequence motifs: NRHAKTA and HLG.
YppF-like protein (YppF)
Type: Family

The YppF-like protein family includes the B. subtilis YppF protein

, which is functionally uncharacterised. Proteins in this family are approximately 60 amino acids in length and contain a conserved LLDF sequence motif.
Domain of unknown function DUF4140 (DUF4140)
Type: Domain

This N-terminal domain of unknown function is often found with DUF4139 (

).
YppG-like protein (YppG)
Type: Family

The YppG-like protein family includes the B. subtilis YppG protein

, which is functionally uncharacterised. Proteins in this family are typically between 115 and 181 amino acids in length and contain two completely conserved residues (F and G) that may be functionally important.
Protein of unknown function DUF4282 (DUF4282)
Type: Family

This family of proteins is functionally uncharacterised. Proteins in this family contain is a single completely conserved residue E that may be functionally important.
Domain of unknown function DUF4283 (DUF4283)
Type: Domain

This domain is found in plant proteins including the uncharacterised protein At4g02000. Considering the very diverse range of other domains it is associated with, it is possible that this domain is a binding/guiding region. It contains two highly conserved tryptophan residues.
Enhanced intracellular survival protein domain (Eis_dom)
Type: Domain

This domain is found in enhanced intracellular survival protein eis from Mycobacterium tuberculosis. It shares protein sequence similarity with the SCP2 sterol-binding domain.
Immunity protein 22 (Imm22)
Type: Family

This entry represents a predicted immunity protein with an α+β fold and conserved tryptophan,tyrosine and an acidic residues. Proteins containing this domain are present in bacterial polymorphic toxin systems as an immediate gene neighbour of the toxin gene, which usually contains toxin domains of the ColD/E5, Tox-REase-4, Ntox49 or Ntox14 families . The domain is also found in heterogeneous polyimmunity loci.
Kinase suppressor of RAS, SAM-like domain (KSR_SAM-like_dom)
Type: Domain

This SAM-like domain is found in kinase suppressor of Ras proteins, which are location-regulated scaffolding proteins connecting MEK to RAF . This domain is part of the N-terminal regulatory region that mediates heterodimerization of BRAF with KSR1.
Type VI secretion system (T6SS), amidase effector protein 4 (Tae4)
Type: Family

Tae4 is a new form of toxin-antitoxin system protein for a type VI secretion system, T6SS. T6SS has roles in interspecies interactions, as well as higher order host-infection, by injecting effector proteins into the periplasmic compartment of the recipient cells of closely related species. Pseudomonas aeruginosa produces at least three effector proteins to other cells and thus has three specific cognate immunity proteins to protect itself. Tae4, or type VI amidase effector 4, in Enterobacter cloacae has a cognate Tai4 or type VI amidase immunity 4 protein .
Protein of unknown function DUF4286 (DUF4286)
Type: Family

This family of proteins is functionally uncharacterised.
Cyanobacterial aminoacyl-tRNA synthetase, CAAD domain (CAAD_dom)
Type: Domain

This domain is present in aminoacyl-tRNA synthetases (aaRSs), enzymes that couple tRNAs to their cognate amino acids . aaRSs from cyanobacteria containing the CAAD (for cyanobacterial aminoacyl-tRNA synthetases appended domain) protein domains are localised in the thylakoid membrane. The domain bears two putative transmembrane helices and is present in glutamyl-, isoleucyl-, leucyl-, and valyl-tRNA synthetases, the latter of which has probably recruited the domain more than once during evolution.
Domain of unknown function DUF4328 (DUF4328)
Type: Domain

This domain is functionally uncharacterised. It is found in proteins from bacteria.
Protein of unknown function DUF4331 (DUF4331)
Type: Family

This family of bacterial proteins is functionally uncharacterised. Proteins in this family contain a conserved FPY sequence motif.
Domain of unknown function DUF4332 (DUF4332)
Type: Domain

This presumed domain of unknown function is sometimes found on its own in uncharacterised bacterial proteins, and can also be found at the C terminus of Lysine-tRNA ligases and other proteins.
Domain of unknown function DUF4334 (DUF4334)
Type: Domain

This domain is found in bacteria and eukaryotes, and is approximately 60 amino acids in length. This domain is frequently found at the C terminus of

.
Protein of unknown function DUF4335 (DUF4335)
Type: Family

This family of proteins is functionally uncharacterised. Proteins in this family acontain two completely conserved residues (G and D) that may be functionally important.
Protein of unknown function DUF4337 (DUF4337)
Type: Family

This family of proteins is functionally uncharacterised. Proteins in this family are found in bacteria and contain a single completely conserved residue Q that may be functionally important.
YqfQ-like protein (YqfQ)
Type: Family

The YqfQ-like protein family includes the B. subtilis YqfQ protein

, also known as VrrA, which is functionally uncharacterised. Proteins in this family are typically between 146 and 237 amino acids in length and contain two conserved sequence motifs: QYGP and PKLY.
YgaB-like protein (YgaB)
Type: Family

The YgaB-like protein family includes the B. subtilis YgaB protein

, which is functionally uncharacterised.
YwpF-like protein (YwpF)
Type: Family

The YwpF-like protein family includes the B. subtilis YwpF protein

, which is functionally uncharacterised. Proteins in this family are typically between 146 and 167 amino acids in length and contain a conserved IIN sequence motif.
Nucleoporin FG repeat (Nucleoporin_FG_rpt)
Type: Repeat

This entry represents a region containing FG repeats that is found in nucleoporin proteins, key elements of the selective gate-barrier that limits the diffusion of cargoes through the NPC . It includes the yeast nucleoporins Nup116, Nup100, Nup49, Nup57 and Nup 145.
DpnD/PcfM-like, C-terminal domain (DpnD/PcfM_C)
Type: Domain

This entry represents a presumed domain found at the C-terminal of a group of functionally uncharacterised proteins from bacteria. There are two completely conserved residues (E and A) that may be functionally important.
YwiC-like protein (YwiC)
Type: Family

The YwiC-like protein family includes the B. subtilis YwiC protein

, which is functionally uncharacterised. There is a single completely conserved residue G that may be functionally important.
FlxA-like protein (FlxA)
Type: Family

This family includes FlxA from E. coli (

) and related sequences. The expression of FlxA is regulated by the FliA sigma factor, a transcription factor specific for class 3 flagellar operons. However FlxA is not required for flagellar function or formation .
Protein of unknown function DUF4359 (DUF4359)
Type: Family

This family of bacterial proteins is functionally uncharacterised. Proteins in this family contain two completely conserved residues (P and S) that may be functionally important.
Domain of unknown function DUF4357 (DUF4357)
Type: Domain

This domain is found in bacteria and archaea. In this domain there are two completely conserved residues (G and W) that may be functionally important.
Capsid assembly scaffolding protein Gp46 (Gp46)
Type: Family

This entry includes the capsid assembly scaffolding protein Gp46 from Staphylococcus phage 80alpha, which is involved in icosahedric procapsid assembly. It coassembles with capsid proteins to form the procapsid . The scaffolding protein is found within the capsid as a series of concentric shells. During DNA packaging, the scaffolding protein molecules are released from the procapsid.
Protein of unknown function DUF4354 (DUF4354)
Type: Family

Several members of this family are annotated as being ATP/GTP-binding site motif A (P-loop) proteins, but this has not been confirmed. The one structure solved for this family (

) exhibits an immunoglobin-like β-sandwich fold. Crystal packing suggests that a tetramer is a significant oligomerisation state, and a disulphide bridge is formed between Cys 125 at the C-terminal end of the monomer, and Cys 69.
YARHG domain (YARHG_dom)
Type: Domain

This presumed extracellular domain is about 70 amino acids in length. It is named YARHG after a conserved motif in the sequence. This domain is associated with peptidases and bacterial kinase proteins. Its molecular function is unknown.
HMG-CoA reductase, N-terminal domain (HMG-CoA_N_dom)
Type: Domain

This domain is found at the N terminus of fungal 3-hydroxy-3-methylglutaryl-coenzyme A (HMG-CoA) reductase, which catalyses the conversion of HMG-CoA to mevalonate. There is a well-conserved characteristic HPIH motif, but the function of the domain is not known.
Carbohydrate-binding domain-containing protein Cthe_2159 (Cthe_2159)
Type: Family

Cthe_2159 from Clostridium thermocellum is the first representative of a novel family of cellulose and/or acid-sugar binding β-helix proteins that share structural similarities with polysaccharide lyases .
Photosystem II Psb27 (PSII_Psb27)
Type: Family

This entry represents Psb27, a small thylakoid lumen-localised protein known to serve as an assembly factor for the biogenesis and repair of the PSII complex . Psb27 is comprised of four helices arranged in a right handed up-down-up-down fold, with a less ordered region located at the N-terminal .
PcfJ-like protein (PcfJ)
Type: Family

The PcfJ-like protein family includes the E. faecalis PcfJ protein

, which is functionally uncharacterised. There is a conserved HCV sequence motif.
Domain of unknown function DUF4351 (DUF4351)
Type: Domain

This uncharacterised domain is found in bacteria.
YcxB-like, C-terminal domain (YcxB-like_C)
Type: Domain

This entry represents the C-terminal domain of the B. subtilis YcxB protein

, which is a functionally uncharacterised transmembrane protein, and similar bacterial sequences.
Topoisomerase C-terminal repeat (Toprim_C_rpt)
Type: Repeat

This domain occurs in the C terminus of a number of DNA topoisomerases 1. It is sometimes found repeated.
Protein of unknown function DUF4348 (DUF4348)
Type: Family

This family of bacterial proteins is functionally uncharacterised.
RloB-like protein (RloB)
Type: Family

This family includes the RloB protein that is found within a bacterial restriction modification operon. It also includes the AbiLii protein that is found as part of a plasmid encoded phage abortive infection mechanism . Deletion of part of the abiLii gene was sufficient to abolish phage resistance. Other proteins in this family are annotated as CRISPR Csm2 proteins.
Domain of unknown function DUF4347 (DUF4347)
Type: Domain

This uncharacterised domain contains two completely conserved residues (C and G) that may be functionally important.
Growth arrest-specific protein 8 domain (GAS8_dom)
Type: Domain

This is the highly conserved central region of Gas8 proteins. Growth arrest-specific protein 8 (Gas8) is a microtubule-binding protein localised to regions of dynein regulation in mammalian cells. In mouse, Gas8 is predominantly a testicular protein, whose expression is developmentally regulated during puberty and spermatogenesis. In humans, it is absent in infertile males who lack the ability to generate gametes. The localisation of Gas8 in the motility apparatus of post-meiotic gametocytes and mature spermatozoa, together with the detection of Gas8 also in cilia at the apical surfaces of epithelial cells lining the pulmonary bronchi and Fallopian tubes suggests that the Gas8 protein may have a role in the functioning of motile cellular appendages .
YebO-like protein (YebO)
Type: Family

This family of proteins includes YebO, which is functionally uncharacterised. Their distribution suggests that they may be of phage origin.
PterinBD-DUF4346 (PterinBD-DUF4346)
Type: Domain

This domain is found in bacteria, archaea and a few lower eukaryotes species. There are two conserved sequence motifs: LDP and DHA. Many members of this family have been annotated as dihydropteroate synthases, however no experimental evidence can be found for this and

has been shown not to possess dihydropteroate synthase activity . In bacteria, this domain is found in predicted conflict systems that also encode genes for an active Thymidylate synthase and a pterin-dependent one-carbon carrier (MtrA domain). This system is predicted to deplete virally generated nucleotides and replace them with a nucleotide that restricts invasive DNA or protects host DNA .
YedD-like protein (YedD)
Type: Family

This family of proteins includes the uncharacterised lipoprotein YedD.
Protein of unknown function DUF4345 (DUF4345)
Type: Family

This family of proteins is uncharacterised. Proteins in this family contain a single completely conserved residue E that may be functionally important.
YjcZ-like protein (YjcZ)
Type: Family

This family of proteins is functionally uncharacterised. It includes YjcZ protein from E. coli (

) and related sequences. There are two conserved sequence motifs: FGD and MPR.
YccJ-like protein (YccJ)
Type: Family

The YccJ-like family of proteins is named after the functionally uncharacterised E. coli YccJ protein (

) .
ATP-binding sugar transporter-like protein (ATP-bd_sugar_transptr-like)
Type: Family

Members of this family are putative ATP-binding sugar transporter-like protein. This entry also includes the phage Head-tail joining protein, known as Gp10 from Bacteriophage N15. It plays a role in virion assembly by joining the head and the tail at the last step of morphogenesis.
BCP1 family (BCP1_family)
Type: Family

This family of proteins includes BRCA2 and CDKN1A-interacting protein (BCCIP) and Bcp1. In fungi, Bcp1 is involved in nuclear export, actin cytoskeleton organisation and vesicular transport . Its homologue in human and mouse, BCCIP, may promote cell cycle arrest by enhancing the inhibition of CDK2 activity by CDKN1A/p21 and may be required for repair of DNA damage by homologous recombination in conjunction with BRCA2 .
YebF/Colicin-M immunity protein (YebF/ColM_immunity)
Type: Family

This family includes the colicin M immunity protein Cmi, and the protein of unknown function YebF. Cmi protects cells from the colicin M toxin, though the mechanism by which it achieves this is not known . The protein forms an α-β fold and contains a disulphide bond that is essential for function . Although the function of YbeF is not known, it is secreted by E. coli, and contains the two conserved cysteine residues responsible for the disulphide bond in Cmi .
Actin cytoskeleton-regulatory complex protein End3 (End3)
Type: Family

Endocytosis is accomplished through the sequential recruitment at endocytic sites of proteins that drive cargo sorting, membrane invagination and vesicle release . End3 forms a complex with Pan1 and Sla1 . This complex plays important roles in organisation of the actin cytoskeleton and endocytosis . This complex is also required for normal cell wall morphogenesis in yeast . The subunits of the Pan1 complex are homologous to mammalian intersectin.
OST-HTH/LOTUS domain (OST-HTH/LOTUS_dom)
Type: Domain

This predicted RNA-binding domain found in insect Oskar and vertebrate TDRD5/TDRD7 proteins that nucleate or organise structurally related ribonucleoprotein (RNP) complexes, the polar granule and nuage, is poorly understood . The domain adopts the winged helix-turn-helix fold and binds RNA with a potential specificity for dsRNA . In eukaryotes, this domain is often combined in the same polypeptide with protein-protein- or lipid- interaction domains that might play a role in anchoring these proteins to specific cytoskeletal structures. Thus, proteins with this domain might have a key role in the recognition and localisation of dsRNA, including miRNAs, rasiRNAs and piRNAs hybridized to their targets. In other cases, this domain is fused to ubiquitin-binding, E3 ligase and ubiquitin-like domains, indicating a previously under-appreciated role for ubiquitination in regulating the assembly and stability of nuage-like RNP complexes. Both bacteria and eukaryotes encode a conserved family of proteins that combines this predicted RNA-binding domain with a previously uncharacterised RNAse domain belonging to the superfamily that includes the 5'->3' nucleases, PIN and NYN domains .
NLPC/P60, N-terminal domain (NLPC/P60_N_dom)
Type: Domain

This domain is found at the N terminus of

, which is a four-domain protein that possesses a C-terminal NLP/P60 domain (

). The N-terminal domain appears to act as a stabilising domain.
Large ribosomal subunit protein uL18, C-terminal, eukaryotes (Ribosomal_uL18_C_euk)
Type: Domain

This entry represents the C-terminal domain of the large ribosomal subunit protein uL18 (also known as L5) from eukaryotes.
TcpE family (TcpE)
Type: Family

This family of proteins includes TcpE, a bacterial conjugative transposon membrane protein.
Lsm14-like, N-terminal (Lsm14-like_N)
Type: Domain

The Lsm14 N-terminal domain is a type of LSM domain found in Lsm14 proteins (also known as Rap55) and in the Saccharomyces cerevisiae homologue Scd6 . The domain is also found in the human EDC3 protein (enhancer of mRNA-decapping protein 3) where it is fused to the the Rossmanoid YjeF-N domain . In addition, both EDC3 and Scd6 are found fused to the FDF domain .
Transcription factor MYC/MYB N-terminal (MYC/MYB_N)
Type: Domain

This is the N-terminal region of a family of MYB and MYC transcription factors. The DNA-binding HLH domain is further downstream,

. Members of the MYB and MYC family regulate the biosynthesis of phenylpropanoids in several plant species .
YobH-like protein (YobH)
Type: Family

The YobH-like protein family includes the YobH protein from E. coli

, which is functionally uncharacterised. Proteins in this family are approximately 80 amino acids in length and contain two conserved sequence motifs: GYG and GLGL.
YqjK-like protein (YqjK)
Type: Family

The YqjK-like protein family includes the E. coli YqjK protein

, which is functionally uncharacterised. There is a single completely conserved residue R that may be functionally important.
YlbE-like protein (YlbE)
Type: Family

The YlbE-like protein family includes the B. subtilis protein YlbE

, which is functionally uncharacterised. Proteins in this family are approximately 80 amino acids in length and contain a conserved WYR sequence motif.
Cell morphogenesis protein N-terminal (Cell_morpho_N)
Type: Domain

This entry represents the conserved N-terminal domain of proteins that are involved in cell morphogenesis. Among these are furry proteins and homologues , and proteins PAG1 and Mor2 .
TILa domain (TILa_dom)
Type: Domain

This cysteine rich domain often occurs along side the TIL domain (

) and may be a distantly related relative.
YpjP-like protein (YpjP)
Type: Family

The YpjP-like protein family includes the B. subtilis YpjP protein

, which is functionally uncharacterised.
YqzL-like protein (YqzL)
Type: Family

The YqzL-like protein family includes the B. subtilis YqzL protein

, which is functionally uncharacterised.
YtpI-like protein (YtpI)
Type: Family

The YtpI-like protein family includes the B. subtilis YtpI protein

, which is functionally uncharacterised.
YlzJ-like protein (YlzJ)
Type: Family

The YlzJ-like protein family includes the B. subtilis YlzJ protein

, which is functionally uncharacterised. Proteins in this family are typically between 61 and 72 amino acids in length and contain two completely conserved residues (L and G) that may be functionally important.
YlaH-like protein (YlaH)
Type: Family

The YlaH-like protein family includes the B. subtilis YlaH protein

, which is functionally uncharacterised.There is a conserved LGFA sequence motif.
YoqO-like protein (YoqO)
Type: Family

The YoqO-like protein family includes the B. subtilis YoqO protein

, which is functionally uncharacterised. There are two completely conserved residues (I and Y) that may be functionally important.
YqzE-like protein (YqzE)
Type: Family

The YqzE-like protein family includes the B. subtilis YqzE protein

, which is functionally uncharacterised. It is a part of the ComG operon, which is regulated by the competence transcription factor ComK .
YusW-like protein (YusW)
Type: Family

The YusW-like protein family includes the B. subtilis YusW protein

, which is functionally uncharacterised.
PcfK-like protein (PcfK)
Type: Family

The PcfK-like protein family includes the Enterococcus faecalis PcfK protein

, which is functionally uncharacterised. There are two completely conserved residues (D and L) that may be functionally important.
YuzL-like protein (YuzL)
Type: Family

The YuzL-like protein family, which is functionally uncharacterised, includes the B. subtilis YuzL protein

.
YyzF-like protein (YyzF)
Type: Family

The YyzF-like protein family, which is functionally uncharacterised, includes the B. subtilis YyzF protein

.
YfzA-like protein (YfzA)
Type: Family

The YfzA-like protein family, which is functionally uncharacterised, includes the B. subtilis YfzA protein

.
Protein of unknown function DUF4287 (DUF4287)
Type: Family

The function of these proteins is not known.
Protein of unknown function DUF4288 (DUF4288)
Type: Family

The function of these proteins is not known.
Putative porin-10 (Porin_10)
Type: Family

This family of membrane β-barrel proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 655 and 722 amino acids in length.

is identified by Gene3D as a membrane bound β-barrel. These sequences are putative porins.
Protein of unknown function DUF4290 (DUF4290)
Type: Family

This family of proteins is functionally uncharacterised. There are two conserved sequence motifs: EYGR and KLWD.
Protein of unknown function DUF4291 (DUF4291)
Type: Family

This family of proteins is functionally uncharacterised. There are two conserved sequence motifs: VYQAY and RMTW.
Protein of unknown function DUF4292 (DUF4292)
Type: Family

The function of these proteins is not known.
Protein of unknown function DUF4293 (DUF4293)
Type: Family

The function of these proteins is not known.
Protein of unknown function DUF4294 (DUF4294)
Type: Family

The function of these proteins is not known.
Domain of unknown function DUF4333 (DUF4333)
Type: Domain

This domain is functionally uncharacterised. There are two completely conserved C residues that may be functionally important.
Protein of unknown function DUF4336 (DUF4336)
Type: Family

The function of these proteins is not known.
Druantia protein DruA (DruA)
Type: Family

Druantia type I is an antiviral defense system composed of DruA, DruB, DruC, DruD and DruE. Expression of Druantia in E.coli (strain MG1655) confers resistance to phage lambda, SECphi18, SECphi27 and T4. This entry represents DruA .