SII-SWORD/CoKE huggingface dataset:
Pfam PF14913: DPCD protein family (family)
This protein is a found in eukaryotes and a mutation in this protein is thought to cause Primary Ciliary Dyskinesia (PCD). This protein is 203 amino acids in length, 23 kDa in size and its function remains unknown. The gene that encodes this protein is a candidate gene for PCD and is expressed during ciliogenesis. PCD affects the airways and reproductive organs, and probing Northern blots show DPCD expression in humans is highest in the testes. Additionally, there is no indication of major splice variants.
Pfam PF14973: TERF1-interacting nuclear factor 2 N-terminus (family)
This is the N-terminus of TERF1-interacting nuclear factor 2. It is required for the formation of the shelterin complex. The shelterin complex is involved in the protection and maintenance of telomeres.
Pfam PF22672: Duffy-binding-like domain, C-terminal subdomain (domain)
This entry represents a domain found C-terminally to Duffy binding-like (DBL) domains of PfEMP1, the adhesin of Plasmodium falciparum which is an important target for protective immunity and is implicated in the pathology of malaria through its ability to adhere to host endothelial receptors. This domain consists of an helical bundle.
Pfam PF11957: THO complex subunit 1 transcription elongation factor (family)
The THO complex plays a role in coupling transcription elongation to mRNA export.  It is composed of subunits THP2, HPR1, THO2 and MFT1. The THO complex is a nuclear complex that is required for transcription elongation through genes containing tandemly repeated DNA sequences. The THO complex is also part of the TREX (TRanscription EXport) complex that is involved in coupling transcription to export of mRNAs to the cytoplasm.
Pfam PF17841: BID domain of Bartonella effector protein (Bep) (domain)
This entry is the BID (Bep intracellular delivery) domain located at the C-terminal of Bartonella effector proteins (Beps). It functions as a secretion signal in a subfamily of protein substrates of bacterial type IV secretion (T4S) systems. It mediates transfer of (1) relaxases and the attached DNA during bacterial conjugation, and (2) numerous Beps during protein transfer into host cells infected by pathogenic Bartonella species. Crystal structure of several representative BID domains show a conserved fold characterized by a compact, antiparallel four-helix bundle topped with a hook.
Pfam PF22766: ZW10 C-terminal helical domain (repeat)
This entry represents the last of the alpha-helical repeat domains of Zw10 protein. Zw10 protein, in the context of the conserved Rod-Zwilch-Zw10 (RZZ) complex, is required for correct metaphase check-pointing during mitosis and it is also important in vesicle transport between Golgi and ER as part of a second complex together with the conserved conserved RINT1/Tip20p and NAG/Sec39p proteins. Zw10 is the metazoan homologue of yeast Dsl1, both included in the complexes associated with tethering containing helical rods (CATCHR) family, sharing structural features.
Pfam PF03767: HAD superfamily, subfamily IIIB (Acid phosphatase) (family)
This family proteins includes acid phosphatases and a number of vegetative storage proteins.
Pfam PF10648: Immunoglobulin-like domain of bacterial spore germination (domain)
This domain is found linked to the GerMN domain [pfam:PF10646] in some bacterial proteins. It is predicted to contain an immunoglobulin-like all-beta fold.
Pfam PF13773: Domain of unknown function (DUF4170) (family)
The function of these proteins is not 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 PF10571: Uncharacterised protein family UPF0547 (domain)
This domain contains a zinc-ribbon motif.
Pfam PF15969: Intracellular sensor of Lambda phage, Abi component (family)
RexA is a family of bacterial anti-phage proteins. It forms one partner in the two-component abortive infection system, Abi, of E. coli in partnership with RexB, a membrane-anchored ion- channel. Two RexA are needed to activate one RexB, and activation causes opening of the channel, the efflux of cations, a drop in cellular levels of ATP and subsequent death of the host cell and abortion of the phage infecting process which requires ATP.
Pfam PF11288: Protein of unknown function (DUF3089) (domain)
This family of proteins has no known function but appears to have an alpha/beta hydrolase domain and so is likely to be enzymatic.
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 PF03872: Anti sigma-E protein RseA, N-terminal domain (domain)
Sigma-E is important for the induction of proteins  involved in heat shock response. RseA binds sigma-E via its N-terminal domain, sequestering sigma-E and  preventing transcription from heat-shock promoters. The C-terminal domain is located in the periplasm, and may interact with other protein that signal periplasmic stress.
Pfam PF18964: Family of unknown function (DUF5704) (family)
This entry is mainly found in Firmicutes and has a notable number of highly conserved aromatic amino acids. The entry is found towards the C-terminus of PFAM:PF02368 in some of the members and there are members that present two copies.
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 PF05118: Aspartyl/Asparaginyl beta-hydroxylase (domain)
Iron (II)/2-oxoglutarate (2-OG)-dependent oxygenases catalyse oxidative reactions in a range of metabolic processes.  Proline 3-hydroxylase hydroxylates proline at position 3, the first of a 2-OG oxygenase catalysing oxidation of a free alpha-amino acid. The structure of proline 3-hydroxylase contains the conserved motifs present in other 2-OG oxygenases including a jelly roll strand core and residues binding iron and 2-oxoglutarate, consistent with divergent evolution within the extended family. This family represent the arginine, asparagine and proline hydroxylases. The aspartyl/asparaginyl beta-hydroxylase ([ec:1.14.11.16]) specifically hydroxylates one aspartic or asparagine residue in certain epidermal growth factor-like domains of a number of proteins.
Pfam PF09397: Ftsk gamma domain (domain)
This domain directs oriented DNA translocation and forms a winged helix structure.  Mutated proteins with substitutions in the FtsK gamma DNA-recognition helix are impaired in DNA binding.
Pfam PF20269: CASPASE and TPR Repeat-Associated N-terminal domain (domain)
One of two constant domains forming the CATRA module which is in turn C-terminally fused to a diverse range of conflict effector domains. This gene, along with a gene encoding the CATASP domain and a gene encoding a TPR repeat region fused to a CASPASE domain, forms the three gene island making up the CATRA conflict systems. This alpha/beta domain is predicted to be involved in recognition of invasive molecules or in the transmitting of a signal through conformational change, enabling CASPASE-mediated proteolysis to free the fused effector domains.
Pfam PF11019: Protein of unknown function (DUF2608) (family)
This family is conserved in Bacteria. The function is not 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 PF19930: Family of unknown function (DUF6393) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). 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.
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 PF06350: Hormone-sensitive lipase (HSL) N-terminus (family)
This family consists of several mammalian hormone-sensitive lipase (HSL) proteins ([ec:3.1.1.-]). Hormone-sensitive lipase, a key enzyme in fatty acid mobilisation, overall energy homeostasis, and possibly steroidogenesis, is acutely controlled through reversible phosphorylation by catecholamines and insulin.
Wikipedia: Hormone-sensitive lipase (EC 3.1.1.79, HSL), also previously known as cholesteryl ester hydrolase (CEH), sometimes referred to as triacylglycerol lipase, is an enzyme that, in humans, is encoded by the LIPE gene, and catalyzes the following reaction:(1) diacylglycerol + H2O = monoacylglycerol + a carboxylate
(2) triacylglycerol + H2O = diacylglycerol + a carboxylate
(3) monoacylglycerol + -H2O = glycerol + a carboxylate
Pfam PF19031: First Longin domain of INTU, CCZ1 and HPS4 (domain)
This entry is specific to the first Longin domain of the HerMon (Hermansky-Pudlak syndrome and MON1/CCZ1) family, including protein sequences of INTU, CCZ1 and HPS4 families. The Mon1/Ccz1 complex (MC1) is the GDP/GTP exchange factor (GEF) for the Rab GTPase Ypt7/Rab7 during vesicular trafficking. The Hps1/Hps4 complex (BLOC-3) is a Rab32 and Rab38 GEF and is required for biogenesis of melanosomes and platelet dense granules. Inturned (INTU) and Fuzzy (FUZ) proteins interact as members of the ciliogenesis and planar polarity effector (CPLANE) complex that controls recruitment of intraflagellar transport machinery to the basal body of primary cilia.
Pfam PF11349: Protein of unknown function (DUF3151) (family)
This family of proteins with unknown function appears to be restricted to Actinobacteria.
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 PF18821: Large polyvalent protein-associated domain 7 (domain)
This domain contains conserved aspartate and phenylalanine residues. It is widely present in polyvalent proteins and gene neighbourhoods of conjugative elements. This domain is also known as PTox1.
Pfam PF01488: Shikimate / quinate 5-dehydrogenase (family)
This family contains both shikimate and quinate dehydrogenases. Shikimate 5-dehydrogenase catalyses the conversion of  shikimate to 5-dehydroshikimate. This reaction is part of  the shikimate pathway which is involved in the biosynthesis of aromatic amino acids. Quinate 5-dehydrogenase catalyses the conversion of quinate to 5-dehydroquinate. This reaction is part of the quinate pathway where quinic acid is exploited as a source of carbon in prokaryotes and microbial eukaryotes. Both the shikimate and quinate pathways share two common pathway metabolites 3-dehydroquinate and dehydroshikimate.
Wikipedia: In enzymology, a shikimate dehydrogenase (EC 1.1.1.25) is an enzyme that catalyzes the chemical reactionshikimate + NADP+  3-dehydroshikimate + NADPH + H+
Pfam PF10172: Det1 complexing ubiquitin ligase (family)
DDA1 (De-etiolated 1, Damaged DNA binding protein 1 associated 1) protein binds strongly with DDB1 and Det1 forming a DDD complex which is part of the ubiquitin conjugation system.
Pfam PF00552: Integrase DNA binding domain (domain)
Integrase mediates integration of a DNA copy of the viral genome into the host chromosome.  Integrase is composed of three domains.  The amino-terminal domain is a zinc binding domain. The central domain is the catalytic domain [pfam:PF00665]. This domain is the carboxyl terminal domain that is a non-specific DNA binding domain.
Wikipedia: Retroviral integrase (IN) is an enzyme produced by a retrovirus that integrates its genetic information into that of the host cell it infects. Retroviral INs are not to be confused with phage integrases (recombinases) used in biotechnology, such as λ phage integrase, as discussed in site-specific recombination.
Pfam PF10488: Phosphatase-1 catalytic subunit binding region (domain)
This conserved C-terminus appears to be a protein phosphatase-1 catalytic subunit (PP1C) binding region, which may in some circumstances also be retroviral in origin since it is found in both herpes simplex virus and in mouse and man. This domain is found in Gadd-34 apoptosis-associated proteins as well as the constitutive repressor of eIF2-alpha phosphorylation/protein phosphatase 1, regulatory (inhibitor) subunit 15b, otherwise known as CReP. Diverse stressful conditions are associated with phosphorylation of the {alpha} subunit of eukaryotic translation initiation factor 2 (eIF2{alpha}) on serine 51. This signaling event, which is conserved from yeast to mammals, negatively regulates the guanine nucleotide exchange factor, eIF2-B and inhibits the recycling of eIF2 to its active GTP bound form. In mammalian cells eIF2{alpha} phosphorylation emerges as an important event in stress signaling that impacts on gene expression at both the translational and transcriptional levels.
Pfam PF12288: Carboxysome shell peptide mid-region (family)
This domain family is found in bacteria and eukaryotes, and is approximately 430 amino acids in length. This family is annotated frequently as a carboxysome shell peptide, however there is little publication to confirm this.
Pfam PF06510: Protein of unknown function (DUF1102) (family)
This family consists of several hypothetical archaeal proteins of unknown function.
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 PF01958: Aspartate dehydrogenase, C-terminal (domain)
This entry represents the C-terminal domain of aspartate dehydrogenases that belong to a unique class of amino acid dehydrogenases. The structure of Thermotoga maritima TM1643 has been found to contain an N-terminal Rossmann fold domain (which binds the NAD(P)+ cofactor) and a C-terminal alpha/beta domain. Enzymatic characterisation of TM1643 revealed that it possesses NAD or NADP-dependent dehydrogenase activity toward L-aspartate but no aspartate oxidase activity. Members of this group share some structural similarity to several other NAD(P)+-dependent oxidoreductases, including inositol 1-phosphate synthase, dihydrodipicolinate reductase, and ASA-DH. It has been proposed that in Thermotoga maritima, TM1643 catalyses the first reaction of de novo biosynthesis of NAD from aspartate, and it produces iminoaspartate required for this pathway.
Pfam PF03044: Herpesvirus UL16/UL94 family (family)
This family groups together HSV-1 UL16 [swissprot:P10200], HSV-6 ORF11R [swissprot:P24442], EHV-1 46 [swissprot:P28970], HCMV UL94 [swissprot:P16800], EBV BGLF2 [swissprot:P03221] and VZV 44 [swissprot:P09293]. UL16 protein may play a role in capsid maturation including DNA packaging/cleavage. In immunofluorescence studies, UL16 was localised to the nucleus of infected cells in areas containing high concentrations of HSV capsid proteins. These nuclear compartments have been described previously as viral assemblons and are distinct from compartments containing replicating DNA. Localisation within assemblons argues for a role of UL16 encoded protein in capsid assembly or maturation.
Pfam PF00932: Lamin Tail Domain (domain)
The lamin-tail domain (LTD), which has an immunoglobulin (Ig) fold, is found in Nuclear Lamins, Chlo1887 from Chloroflexus, and several bacterial proteins where it occurs with membrane associated  hydrolases of the metallo-beta-lactamase,synaptojanin, and  calcineurin-like phosphoesterase superfamilies.
Wikipedia: Intermediate filaments (IFs) are cytoskeletal structural components found in the cells of vertebrates, and many invertebrates. Homologues of the IF protein have been noted in an invertebrate, the cephalochordate Branchiostoma.
Pfam PF05482: Serendipity locus alpha protein (SRY-A) (family)
The Drosophila serendipity alpha (sry alpha) gene is specifically transcribed at the blastoderm stage, from nuclear cycle 11 to the onset of gastrulation, in all somatic nuclei. SRY-A is required for the cellularisation of the embryo and is involved in the localisation of the actin filaments just prior to and during plasma membrane invagination. This family forms a different clade of the Vinculin superfamily with an evolutionary relationship that is functionally consistent with a role for sry alpha at the actin cortex during cellularization.
Pfam PF21422: Orthomyxovirus nucleoprotein, C-terminal (domain)
This entry represents a domain found in the nucleoprotein from the orthomyxovirus Infectious salmon anemia virus. This protein is similar to that in Influenza virus and consists of a head and a body domain. This entry represents the tail loop which plays a role in oligomerisation. It folds into an extended beta-hairpin that protrudes into a deep pocket in a neighbouring subunit to mediate dimer formation.
Pfam PF16306: Domain of unknown function (DUF4948) (family)
This small family consists of uncharacterized proteins around 200 residues in length and is mainly found in various Bacteroides, Paraprevotella, Parabacteroides and Alistipes species. The function of this family is unknown.
Pfam PF15386: Drosophila Tantalus-like (family)
An alpha+beta fold domain found in metazoan proteins such as Drosophila Tantalus. Drosophila Tantalus binds the chromatin protein Additional sex combs (Asx) and also binds DNA in vitro.
Pfam PF05350: Glycogen synthase kinase-3 binding (family)
Glycogen synthase kinase-3 (GSK-3) sequentially phosphorylates four  serine residues on glycogen synthase (GS), in the sequence SxxxSxxxSxxx-SxxxS(p), by recognising and phosphorylating the first  serine in the sequence motif SxxxS(P) (where S(p) represents a  phosphoserine). Interaction of GSK-3 with a peptide derived from GSK-3 binding protein (this family) prevents GSK-3 interaction with Axin. This interaction thereby inhibits the Axin-dependent phosphorylation of  beta-catenin by GSK-3.
Pfam PF05496: Holliday junction DNA helicase RuvB P-loop domain (domain)
The RuvB protein makes up part of the RuvABC revolvasome which catalyses the resolution of Holliday junctions that arise during genetic recombination and DNA repair. Branch migration is catalysed by the RuvB protein that is targeted to the Holliday junction by the structure specific RuvA protein. This family contains the N-terminal region of the protein.
Pfam PF17885: Styrene monooxygenase A putative substrate binding domain (domain)
This domain is found in the 46 kDa FAD-specific styrene epoxidase (SMOA) protein, comprises a part of the styrene monooxygenase (SMO) two-component flavoprotein monooxygenase enzyme. Structural analysis indicates that SMOA monomer comprises two globular domains spanned by a long alpha-helix. This domain contains a putative substrate binding site.
Pfam PF04287: tRNA pseudouridine synthase C (family)
This family is suggested to be the catalytic domain of tRNA pseudouridine synthase C by association. The structure has been solved for one member, as PDB:2HGK, which by inference is designated in this way.
Pfam PF15745: AP-1 complex-associated regulatory protein (family)
AP-1 complex-associated regulatory protein (AP1AR), also known as gadkin or gamma-BAR, is a negative regulator of the actin-related protein (ARP)2/3 complex, a major regulator of actin dynamics. Through inhibition of ARP2/3, gadkin negatively regulates cell spreading and motility . Gadkin is also a modulator of adaptor protein (AP)-1-mediated endosomal membrane trafficking .
Wikipedia: AP-1 complex-associated regulatory protein is a protein that in humans is encoded by the AP1AR gene.
Pfam PF11654: Non-classical export protein 1 (family)
This entry represents the non classical export protein 1 family. Family members are Involved in a novel pathway of export of proteins that lack a cleavable signal sequence.
Pfam PF11539: Protein of unknown function (DUF3228) (family)
This family of proteins has no known function.
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 PF12103: Surface lipoprotein of Spirochaetales order (domain)
Lipl32 is an outer membrane surface lipoprotein of Leptospira like bacteria.
Pfam PF08562: Crisp (domain)
This domain is found on Crisp proteins which contain [pfam:PF00188] and has been termed the Crisp domain. It is found in the mammalian reproductive tract and the venom of reptiles, and has been shown to regulate ryanodine receptor Ca2+ signalling. It contains 10 conserved cysteines which are all involved in disulphide bonds and is structurally related to the ion channel inhibitor toxins BgK and ShK.
Wikipedia: Cysteine-rich secretory proteins, often abbreviated as CRISPs, are a group of glycoproteins. They are a subgroup of the CRISP, antigen 5 and Pr-1 (CAP) protein superfamily and also contain a domain related to the ShK toxins. They are substantially implicated in the functioning of the mammalian reproductive system. CRISPs are also found in a variety of snake venoms where they inhibit both smooth muscle contraction and cyclic nucleotide-gated ion channels.
Pfam PF19343: HAM1-like, N-terminal domain (domain)
This entry represents a domain found at the N-terminal end of the putative cell signalling protein HAM1 from Cryptococcus neoformans and similar fungal sequences. HAM1 may act as a negative regulator of mating during vegetative growth. Proteins with this domain often also contain a C-terminal domain [pfam:PF14613].
Pfam PF18595: Nuf2, DHR10-like domain (domain)
This domain is found at the C-terminal region of Nuf2 proteins. This domain was identified as MazG related domain also designated as Designed helical repeat protein 10 (DHR10) that actually adopts a coiled-coil structure. Nuf2 is part of the Ndc80 complex, which binds to the spindle and is required for chromosome segregation and spindle checkpoint activity.
Pfam PF14770: Transmembrane protein 18 (family)
The function of this family is not known, however it is predicted to be a three-pass membrane protein.