SII-SWORD/CoKE huggingface dataset:
Pfam PF09125: Cytochrome C oxidase subunit II, transmembrane (domain)
Members of this family adopt a tertiary structure consisting of two antiparallel transmembrane helices, in a transmembrane helix hairpin fold.
Pfam PF24322: T6SS Tle3 phospholipase effector domain (domain)
This entry represents an alpha/beta domain found in the type VI secretion system (T6SS) Tle3 phospholipase effector from adherent-invasive Escherichia coli and related proteins. Tle3 has a phospholipase A1 activity and its toxicity is neutralised by the cognate immunity protein Tli3. Tli3 and Tle3 form a stable complex in which a loop of Tli3 inserts deeply in the Tle3 substrate-binding pocket and thus inhibiting its function. This Tle3 domain folds into a globular alpha/beta structure consisting of a central beta-sheet and alpha-helices packed on both sides. It contains the typical nucleophile-elbow motif and structurally resembles classical alpha/beta hydrolase fold but elaborated with a number of large loops.
Pfam PF12274: Protein of unknown function (DUF3615) (family)
This domain family is found in bacteria and eukaryotes, and is typically between 86 and 97 amino acids in length. There is a conserved FAE sequence motif. There is a single completely conserved residue F that may be functionally important.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF08244: Glycosyl hydrolases family 32 C terminal (domain)
This domain corresponds to the C terminal domain of glycosyl hydrolase family 32.  It forms a beta sandwich module.
Wikipedia: In molecular biology, glycoside hydrolase family 32 is a family of glycoside hydrolases EC 3.2.1., which are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycoside hydrolases, based on sequence similarity, has led to the definition of &gt;100 different families. This classification is available on the CAZy web site, and also discussed at CAZypedia, an online encyclopedia of carbohydrate active enzymes.
Pfam PF01595: Cyclin M transmembrane N-terminal domain (domain)
This transmembrane domain is found in metal transporter proteins such as cyclin M 1/2 (CNNM). CNNMs are integral membrane proteins that are conserved from bacteria to humans. CNNM family members influence metal ion homeostasis through mechanisms that may not involve direct membrane transport of the ions. Structurally, CNNMs are complex proteins that contain an extracellular N-terminal domain preceding a transmembrane domain, a 'Bateman module', which consists of two cystathionine- beta-synthase (CBS) domains [pfam:PF00571], and a C-terminal cNMP (cyclic nucleotide monophosphate) binding domain. This entry describes the CNNM transmembrane domain which contains four hydrophobic regions and forms a dimer through hydrophobic contacts between TM2 and TM3, in which each chain is composed of three transmembrane helices (TM1-3), a pair of short helices exposed on the intracellular side, and a juxtamembrane (JM) helix that forms a belt-like structure. The homodimer adopts an inward-facing conformation with a negatively charged cavity containing a conserved pi-helical turn in TM3 that coordinates a Mg2 ion.
Pfam PF00215: Orotidine 5'-phosphate decarboxylase / HUMPS family (domain)
This family includes Orotidine 5'-phosphate decarboxylase enzymes [ec:4.1.1.23] that are involved in the final step of pyrimidine biosynthesis. The family also includes enzymes such as hexulose-6-phosphate synthase. This family appears to be distantly related to [pfam:PF00834].
Pfam PF01420: Type I restriction modification DNA specificity domain (domain)
This domain is also known as the target recognition domain (TRD). Restriction-modification (R-M) systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification.  The host genome is protected from cleavage by methylation of specific nucleotides in the target sites.  In type I systems, both restriction and modification activities are present in one heteromeric enzyme complex composed of one DNA specificity subunit (this family), two modification (M) subunits and two restriction (R) subunits.
Pfam PF10744: Mediator of RNA polymerase II transcription subunit 1 (domain)
Mediator complexes are basic necessities for linking transcriptional regulators to RNA polymerase II.  This domain, Med1, is conserved from plants to fungi to humans and forms part of the Med9 submodule of the Srb/Med complex. it is one of three subunits essential for viability of the whole organism via its role in environmentally-directed cell-fate decisions. Med1 is part of the tail region of the Mediator complex.
Wikipedia: Mediator of RNA polymerase II transcription subunit 1 also known as DRIP205 or Trap220 is a subunit of the Mediator complex and is a protein that in humans is encoded by the MED1 gene. MED1 functions as a nuclear receptor coactivator.
Pfam PF14235: Domain of unknown function (DUF4337) (coiled_coil)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 187 and 201 amino acids in length. There is a single completely conserved residue Q that may be functionally important.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF08054: Leucine operon leader peptide (family)
This family consists of the leucine operon leader peptide. The leucine operon is involved in the control of the biosynthesis of leucine. Four adjacent leucine codons within the leucine leader RNA are critically important in transcription attenuation-mediated control of leucine operon expression in bacteria. The leader RNA contains translational start and stop signals, a cluster of four leucine codons and overlapping regions of dyad symmetry that are capable of forming stem-and-loop structures.
Pfam PF13280: WYL domain (domain)
WYL is a Sm-like SH3 beta-barrel fold containing domain. It is a member of the WYL-like superfamily, named for three  conserved amino acids found in a subset of the superfamily.  However, these residues are not strongly conserved throughout  the family. Rather, the conservation pattern includes four basic residues and a position often occupied by a cysteine, which are predicted to line a ligand-binding groove typical of the Sm-like SH3 beta-barrels.  A WYL domain protein (sll7009) is a negative regulator of the  I-D CRISPR-Cas system in Synechocystis sp.  It is predicted  to be a ligand-sensing domain that could bind negatively charged  ligands, such as nucleotides or nucleic acid fragments, to  regulate CRISPR-Cas and other defense systems such as the  abortive infection AbiG system.
Pfam PF19356: Domain of unknown function (DUF5933) (domain)
This presumed domain is functionally uncharacterised. This domain family is found in Actinobacteria, and is approximately 140 amino acids in length. The family is found in association with [pfam:PF14378].
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF19362: Family of unknown function (DUF5938) (family)
This presumed domain is functionally uncharacterised. This domain family is found in proteobacteria and actinobacteria, and is approximately 240 amino acids in length. The family is found in association with [pfam:PF03435].
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF07437: YfaZ precursor (family)
This family contains the precursor of the bacterial protein YfaZ (approximately 180 residues long). Many members of this family are hypothetical proteins.
Pfam PF14941: Out at first (domain)
This entry represents the N-terminal BRICHOS-like domain ([pfam:PF04089]) found in OAF protein family. The gene, OAF (out at first), which encodes this protein, has a promoter which may help mediate regulation of neighbouring genes. An alternative name for this protein is HCV NS5A-transactivated protein 13 target protein 2, which stands for Hepatitis C virus nonstructural 5A-transactivated protein 13 target protein 2. NS5A inhibits double-stranded-RNA-activated protein kinase (PKR) activity, which is thought to allow Hepatitis C Virus replication to continue in the presence of an alpha interferon (IFN)induced antiviral response.
Pfam PF10266: Hereditary spastic paraplegia protein strumpellin (family)
This is a family of proteins conserved from plants to humans, in which two closely situated point mutations in the human protein lead to the condition of hereditary spastic paraplegia. Strumpellin contains one known domain called a spectrin repeat that consists of three alpha-helices of a characteristic length wrapped in a left-handed coiled coil. The spectrin proteins have multiple copies of this repeat, which can then form multimers in the cell. Spectrin associates with the cell membrane via spectrin repeats in the ankyrin protein. The spectrin repeat is a structural platform for cytoskeletal protein assemblies.
Pfam PF18842: Large polyvalent protein associated domain 26 (domain)
This is a small alpha-helical domain with two acidic residues conserved in a predicted loop between two of its helices. The domain is mainly found in polyvalent proteins of conjugative elements.
Pfam PF02329: Histidine carboxylase PI chain (domain)
Histidine carboxylase catalyses the formation of histamine from histidine. Cleavage of the proenzyme PI chain yields two subunits,  alpha and beta, which arrange as a hexamer (alpha beta)6.
Wikipedia: The enzyme histidine decarboxylase is transcribed on chromosome 15, region q21.1-21.2, and catalyzes the decarboxylation of histidine to form histamine. In mammals, histamine is an important biogenic amine with regulatory roles in neurotransmission, gastric acid secretion and immune response. Histidine decarboxylase is the sole member of the histamine synthesis pathway, producing histamine in a one-step reaction. Histamine cannot be generated by any other known enzyme. HDC is therefore the primary source of histamine in most mammals and eukaryotes. The enzyme employs a pyridoxal 5'-phosphate (PLP) cofactor, in similarity to many amino acid decarboxylases. Eukaryotes, as well as gram-negative bacteria share a common HDC, while gram-positive bacteria employ an evolutionarily unrelated pyruvoyl-dependent HDC. In humans, histidine decarboxylase is encoded by the HDC gene.
Pfam PF07536: HWE histidine kinase (domain)
Two-component systems, consisting of a histidine kinase and a cognate response regulator protein, represent the best-known apparatus for transducing external cues into a physiological response in bacteria.  The HWE domain is found in a subset of two-component system kinases, belonging to the same superfamily as [pfam:PF00512] and [pfam:PF07568]. The family was defined by the presence of a highly conserved H residue in the kinase domain and a WxE motif in a C-terminal ATPase domain that is related to [pfam:PF02518]. It has been demonstrated to show structural and functional correlation with [pfam:PF07568]. These proteins are found in a variety of alpha- and gamma- proteobacteria, with significant enrichment in the rhizobia.
Pfam PF09976: Tetratricopeptide repeat-like domain (repeat)
This family resembles a single unit of a TPR repeat.
Pfam PF09977: Putative Tad-like Flp pilus-assembly (family)
This domain, found in various hypothetical prokaryotic proteins, is likely to be involved in Flp lius biogenesis.
Pfam PF00621: RhoGEF domain (domain)
Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases Also called Dbl-homologous (DH) domain. It appears that [pfam:PF00169] domains invariably occur C-terminal to RhoGEF/DH domains.
Wikipedia: RhoGEF domain describes two distinct structural domains with guanine nucleotide exchange factor (GEF) activity to regulate small GTPases in the Rho family. Rho small GTPases are inactive when bound to GDP but active when bound to GTP; RhoGEF domains in proteins are able to promote GDP release and GTP binding to activate specific Rho family members, including RhoA, Rac1 and Cdc42.
Pfam PF07264: Sulfate transporter CysZ/Etoposide-induced protein 2.4 (family)
This family contains a number of eukaryotic etoposide-induced 2.4 (EI24) proteins approximately 350 residues long as well as bacterial CysZ proteins (formerly known as DUF540). In cells treated with the cytotoxic drug etoposide, EI24 is induced by p53. It has been suggested to play an important role in negative cell growth control.
Pfam PF17915: Reverse gyrase zinc finger (domain)
This is the N-terminal zinc finger domain present in reverse gyrase proteins. Most reverse gyrases have a conserve the N-terminal zinc finger domain adopting a treble clef fold, suggesting the importance of this domain domain for the proteins function. In addition, these proteins contain a second zinc finger of zinc beta-ribbon type that is grafted into the Toprim domain ([pfam:PF01751]). Deletion of both zinc fingers abolishes supercoiling activity of reverse gyrase. The structure of Thermotoga maritima reverse gyrase shows that the N-terminal zinc finger firmly attaches the H1 (helicase 1) domain to the topoisomerase domain contributing to double-strand DNA (dsDNA) binding.
Pfam PF05781: MRVI1 protein (family)
This family consists of mammalian MRVI1 proteins which are related to the lymphoid-restricted membrane protein (JAW1) and the IP3 receptor associated cGMP kinase substrates A and B (IRAGA and IRAGB). The function of MRVI1 is unknown although mutations in the Mrvi1 gene induces myeloid leukaemia by altering the expression of a gene important for myeloid cell growth and/or differentiation so it has been speculated that Mrvi1 is a tumour suppressor gene. IRAG is very similar in sequence to MRVI1 and is an essential NO/cGKI-dependent regulator of IP3-induced calcium release. Activation of cGKI decreases IP3-stimulated elevations in intracellular calcium, induces smooth muscle relaxation and contributes to the antiproliferative and pro-apoptotic effects of NO/cGMP. Jaw1 is a member of a class of proteins with COOH-terminal hydrophobic membrane anchors and is structurally similar to proteins involved in vesicle targeting and fusion. This suggests that the function and/or the structure of the ER in lymphocytes may be modified by lymphoid-restricted resident ER proteins.
Pfam PF22831: CATSPERB Ig-like domain (domain)
CATSPERB (Cation channel sperm-associated protein subunit beta) is an auxiliary subunit of the CatSper complex which is involved in sperm cell hyperactivation, a process needed for sperm motility which is essential late in the preparation of sperm for fertilisation. This is a multi-domain protein which consists of an N-terminal domain ([pfam:PF21541]), followed by a beta-propeller ([pfam:PF21548]) that is also present in the other auxiliary subunits gamma, delta and epsilon. This entry represents the Ig-like domain of CATSPERB, which, seals the top of the channel together with the Ig-like domains of the other auxiliary subunits.
Pfam PF14455: Predicted metal binding domain (family)
A predicted metal-binding domain that is found in gene-neighborhood associations with genes encoding components of the bacterial homologs of the ubiquitin modification pathway including the E1, E2, JAB  metallopeptidase and ubiquitin proteins. The domain is characterised  by a conserved motif with a CxxxxxEYHxxxxH signature.
Pfam PF22448: RepB DNA-primase C-terminal helical domain (domain)
RepB_primase is a DNA-primase produced by P4-like phages. It is a zinc-independent primase unlike Pri-type primases. It takes up a dumbbell shaped consisting of an N-terminal catalytic domain separated by a long alpha-helix plus tether and a C-terminal helical-bundle domain. Primases are necessary for phage replication.  RepBprime primases such as in this family recognise both ssiA and ssiB, ie only 1 single-stranded primase initiation site on each strand, independently of each other and then synthesise primers that are elongated by DNA polymerase III. The phage is thus replicated exclusively in leading strand mode.
Pfam PF07359: Liver-expressed antimicrobial peptide 2 precursor (LEAP-2) (family)
This family consists of several mammalian liver-expressed antimicrobial peptide 2 (LEAP-2) sequences. LEAP-2 is a cysteine-rich, and cationic protein. LEAP-2 contains a core structure with two disulfide bonds formed by cysteine residues in relative 1-3 and 2-4 positions. LEAP-2 is synthesised as a 77-residue precursor, which is predominantly expressed in the liver and highly conserved among mammals. The largest native LEAP-2 form of 40 amino acid residues is generated from the precursor at a putative cleavage site for a furin-like endoprotease. In contrast to smaller LEAP-2 variants, this peptide exhibits dose-dependent antimicrobial activity against selected microbial model organisms. The exact function of this family is unclear.
Wikipedia: Liver-expressed antimicrobial peptides are a family of mammalian liver-expressed antimicrobial peptides (LEAP). The exact function of this family is unclear.
Pfam PF05930: Prophage CP4-57 regulatory protein (AlpA) (family)
This family consists of several short bacterial and phage proteins which are related to the E. coli protein AlpA. AlpA suppress two phenotypes of a delta lon protease mutant, overproduction of capsular polysaccharide and sensitivity to UV light. Several of the sequences in this family are thought to be DNA-binding proteins.
Pfam PF18304: SabA N-terminal extracellular adhesion domain (domain)
This is the N-terminal extracellular adhesion domain of Sialic acid binding adhesin (SabA) present in Helicobacter pylori. The N-terminal domain of SabA functions as a sugar-binding adhesion domain with conserved disulfide bonds. Notably, these amino acid residues are not only conserved among SabA orthologs but also between SabA and BabA.
Pfam PF14250: AbrB-like transcriptional regulator (family)
This family of DNA-binding proteins is likely to act as a transcriptional regulator. This family does not include E.coli AbrB, [swissprot:P75747], which belongs to [pfam:PF05145].
Pfam PF09369: MrfA Zn-binding domain (domain)
This is the C-terminal MrfA Zn+2-binding domain (MZB, also referred to as DUF1998) which contains a conserved four-cysteine signature motif.  These four Cys reside in a short coil between two alpha-helices and form a metal ion-binding site. This domain is frequently found at the C-terminal of ndNTPases, however, it is also found encoded in a standalone gene, downstream of putative helicase domain-encoding genes associated with bacterial anti-phage defense system DISARM. MrfA (Mitomycin repair factor A, also known as YprA in Bacillus subtilis) is a DNA helicase that supports repair of mitomycin C-induced DNA damage. MrfA homologues are widely distributed in bacteria and are also present in archaea, fungi and plants. The MrfA-homologue in yeast, Hrq1, also reduces mitomycin C sensitivity. Hrq1 has high similarity to human RecQ4 and was therefore assigned to the RecQ-like helicase family. MrfA homologues appear to be missing in Enterobacteria, however, certain pathogenic Escherichia coli and Salmonella strains harbour Z5898-like helicases with this domain.
Pfam PF20597: Putative Ice-binding-like adhesive domain (domain)
This domain is found N-terminal to repeating stalk domains in bacterial surface proteins. The structure model of this domain is highly similar to the Ice_binding adhesive domain ([pfam:PF11999]). However, the bacterial species in which this domain can be found, are less likely to be water-based and thus the function seems unlikely to be ice-binding.  This domain is found in a Bacillus anthracis protein with the gene name BA_0871 or BASH2_04951, which was described to be collagen binding and to be involved in the bacterial pathogenicity.
Pfam PF10807: Protein of unknown function (DUF2541) (family)
This family of proteins with unknown function appears to be restricted to Enterobacteriaceae. All proteins are annotated as YaaI precursor however currently no function is known.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF24740: Domain of unknown function (DUF7691) (domain)
This entry represents a group of uncharacterised bacterial proteins. They share detectable similarity to proteins members of [pfam:PF08974] whose function is unknown. Their predicted structures resemble the structure of DNA mimic protein DMP12 but elaborated with additional alpha helices.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF20537: Domain of unknown function (DUF6752) (domain)
This presumed domain family is functionally uncharacterised. It is found in bacterial proteins and is typically 54 amino acids in length.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.