SII-SWORD/CoKE huggingface dataset:
Pfam PF12196: FHA Ki67 binding domain of hNIFK (domain)
This domain family is found in eukaryotes, and is approximately 40 amino acids in length. The family is found in association with [pfam:PF00076]. There are two conserved sequence motifs: TPVCTP and LERRKS. This domain is found on the human nucleolar protein hNIFK. It binds to the fork-head-associated domain of human Ki67. High-affinity binding requires sequential phosphorylation by two kinases, CDK1 and GSK3, yielding pThr238, pThr234 and pSer230. This interaction is involved in cell cycle regulation.
Wikipedia: MKI67 FHA domain-interacting nucleolar phosphoprotein is a protein that in humans is encoded by the MKI67IP gene.
Pfam PF13314: Domain of unknown function (DUF4083) (family)
This is a family of very short, approximately 60 residue, proteins from Firmicutes, that are all putatively annotated as being MutT/Nudix. However, the characteristic Nudix motif of GX(5)EX(7)REUXEE is absent.
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 PF16507: Proteasome activator complex subunit 4, mid HEAT repeats region (repeat)
The human Proteasome activator complex subunit 4 (PSME4, also known as PA200) and the yeast homologue BLM10 show 32 HEAT repeat-like modules, each comprising two helices joined by a turn, with adjacent repeats connected by a linker. Whereas a standard HEAT repeat is composed of ~50 residues, these HEAT repeats are highly variable. The length of helices ranges from 8 to 35 residues, turns range from 2 to 87 residues, and linkers range from 1 to 88 residues, with the longest linker, between HR21 and HR22, containing additional secondary structures (two strands and three helices). This entry represents the middle ordered region of the three in these proteins. BLM10 is found to surround the proteasome entry pore in the 1.2 MDa complex of proteasome and BLM10 to form a largely closed dome that is expected to restrict access of potential substrates. Thus BLM10 and PSME4 are predominantly nuclear and stimulate the degradation of model peptides, although they do not appear to stimulate the degradation of proteins, recognise ubiquitin, or utilise ATP.
Wikipedia: A HEAT repeat is a protein tandem repeat structural motif composed of two alpha helices linked by a short loop. HEAT repeats can form alpha solenoids, a type of solenoid protein domain found in a number of cytoplasmic proteins. The name "HEAT" is an acronym for four proteins in which this repeat structure is found: Huntingtin, elongation factor 3 (EF3), protein phosphatase 2A (PP2A), and the yeast kinase TOR1. HEAT repeats form extended superhelical structures which are often involved in intracellular transport; they are structurally related to armadillo repeats. The nuclear transport protein importin beta contains 19 HEAT repeats.
Pfam PF18824: Large polyvalent protein-associated domain 11 (domain)
This is an alpha-helical domain with conserved hydrophobic residues. It is found in polyvalent proteins of conjugative elements.
Pfam PF07086: Jagunal, ER re-organisation during oogenesis (family)
Jagunal is an endoplasmic-reticulum (ER)-membrane protein found in eukaryotes. It is involved in reorganising the ER in cells that must increase exocytic membrane traffic during development, that is, in the oocyte during vitellogenesis. It facilitates vesicular traffic in the subcortex.
Pfam PF12637: TSCPD domain (domain)
This family of proteins is found in bacteria, archaea and viruses.  The domain is found in isolation in many proteins where it has a conserved C-terminal motif TSCPD after which the domain is named.  Most copies of the domain possess 4 conserved cysteines that may be part of an Iron-sulfur cluster. This domain is found at the C-terminus of some ribonucleoside-diphosphate reductase enzymes.
Pfam PF11521: C-terminal general transcription factor TFIIE alpha (family)
TFIIE is compiled of two subunits, alpha and beta. This family of proteins are the C terminal domain of the alpha subunit of the protein which is the largest subunit and contains several functional domains which are important for basal transcription and cell growth. The C terminal end of the protein binds directly to the amino-terminal PH domain of p62/Tfb1 (of IIH) which is involved in the recruitment of the general transcription factor IIH to the transcription preinitiation complex. P53 competes for the same binding site as TFIIE alpha which shows their structural similarity. Like p53, TFIIE alpha 336-439 can activate transcription in vivo.
Pfam PF09717: Plasmodium falciparum domain of unknown function (CPW_WPC) (domain)
This group of sequences is defined by a domain of about 61 residues in length with six well-conserved cysteine residues and six well-conserved aromatic sites. The domain can be found in tandem repeats, and is known so far only in Plasmodium falciparum. It is named for motifs of CPxxW and (less well conserved) WPC. Its function is unknown.
Pfam PF02574: Homocysteine S-methyltransferase (family)
This is a family of related homocysteine S-methyltransferases enzymes: 5-methyltetrahydrofolate--homocysteine S-methyltransferases  also known [ec:2.1.1.13],; Betaine--homocysteine S-methyltransferase  (vitamin B12 dependent), [ec:2.1.1.5],; and Homocysteine S-methyltransferase, [ec:2.1.1.10],.
Pfam PF17699: Family of unknown function (DUF5545) (family)
This is a family of unknown function found in primates.
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 PF23014: Tiam1 second PH domain-like (domain)
This entry represents the second PH domain found in TIAM1 proteins.  The TIAM family proteins are guanine nucleotide exchange factors (GEFs) that modulate the activity of RHO-like GTPases, linking extracellular signals to cytoskeletal dynamics. They are involved in various cellular processes, including cell adhesion, migration, and neurite outgrowth. TIAM family members activate GTPases such as RAC1 and CDC42, which are critical for actin cytoskeleton reorganization, lamellipodial formation, and growth cone advancement in neurons. These proteins contribute to synaptic differentiation and are implicated in the development of the cerebral cortex and eye. The TIAM family is characterized by the presence of multiple domains, including PH domains, which are essential for membrane localization and enhancing catalytic activity, and a TSS domain necessary for Rac1 activity and induction of neurite-like structures.
Pfam PF09149: Domain of unknown function (DUF1935) (domain)
Members of this family are found in various bacterial and eukaryotic hypothetical proteins, as well as in the cysteine protease calpain. Their exact function has not, as yet, been defined.
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 PF00549: CoA-ligase (domain)
This family includes the CoA ligases Succinyl-CoA synthetase alpha and beta chains, malate CoA ligase and ATP-citrate lyase. Some members of the family utilise ATP others use GTP.
Pfam PF01393: Chromo shadow domain (domain)
This domain is distantly related to [pfam:PF00385]. This domain is always found in association with a chromo domain.
Wikipedia: In molecular biology, the chromo shadow domain is a protein domain which is distantly related to the chromodomain. It is always found in association with a chromodomain. Proteins containing a chromo shadow domain include Drosophila and human heterochromatin protein Su(var)205 (HP1); and mammalian modifier 1 and modifier 2.
Pfam PF13752: Domain of unknown function (DUF4165) (domain)
This presumed domain is functionally uncharacterised.
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 PF19735: Family of unknown function (DUF6225) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000896) is described by MIBiG as an example of the following biosynthetic class, other (unspecified). It includes a  member from the cycloserine biosynthetic gene cluster from  Streptomyces lavendulae subsp. lavendulae.
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 PF07892: Protein of unknown function (DUF1667) (family)
Hypothetical archaeal and bacterial proteins make up this family. A few proteins are annotated as being potential metal-binding proteins, and in fact the members of this family have four highly conserved cysteine residues, but no further literature evidence was found in this regard.
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 PF03524: Conjugal transfer protein (family)
This family includes type IV secretion system CagX conjugation protein. Other members of this family are involved in conjugal transfer to plant cells of T-DNA.
Pfam PF25067: Med14 RM domain (repeat)
This entry represents a domain found in the human Mediator of RNA polymerase II transcription subunit 14 (Med14) and related proteins. Med14 is a component of the Mediator complex, a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. Mediator is recruited to promoters by direct interactions with regulatory proteins and serves as a scaffold for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. The major portion of Med14 exists in the Head-Shoulder module of the Mediator and consists of nine tandem repeats (RM1 to RM9), which are arranged in an atypical right-handed helix. This entry represents repeat RM5.
Pfam PF08180: B melanoma antigen family (family)
This family consists of the B melanoma antigen (BAGE) peptides. The BAGE gene encodes a human tumour antigen that is recognised by a cytolytic T lymphocyte. BAGE genes are expressed in melanomas,  bladder and lung carcinomas and in a few tumours of other histological  types.
Pfam PF09040: Gastric H+/K+-ATPase, N terminal domain (domain)
Members of this family adopt an alpha-helical conformation under hydrophobic conditions. The domain contains tyrosine residues, phosphorylation of which regulates the function of the ATPase. Additionally, the domain also interacts with various structural proteins, including the spectrin-binding domain of ankyrin III.
Wikipedia: Sodium/potassium-transporting ATPase subunit alpha-1 is an enzyme that in humans is encoded by the ATP1A1 gene.
Pfam PF25044: Domain of unknown function (DUF7789) (domain)
This domain is found in uncharacterised eukaryotic proteins. It is predicted to fold into a four-helical up-and-down bundle. It is usually found in two tandem copies. This domain is likely associated with the membrane.
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 PF21377: MurD N-terminal domain (domain)
This is the N-terminal catalytic domain of MurD ligases.
Pfam PF17561: Type VI secretion system, TssO (family)
T6SSs are toxin delivery systems. It is a multiprotein complex requiring numerous core proteins (Tss proteins) including cytoplasmic, transmembrane, and outer membrane components. The needle or tube apparatus is comprised of a phage-like complex, similar to the T4 contractile bacteriophage tail, which is thought to be anchored to the membrane by a trans-envelope complex. TssO proteins have one predicted TM region near their N-termini. In Flavobacterium johnsoniae, three specific components (TssN, TssO and TssP) are absent in the other sub-types of T6SS.
Pfam PF08527: Protein-arginine deiminase (PAD) middle domain (domain)
This family represents the central non-catalytic domain of protein-arginine deiminase. This domain has an immunoglobulin-like fold.
Pfam PF14534: Domain of unknown function (DUF4440) (domain)
This domain is found in uncharacterised proteins from bacteria, archaea and eukaryotes, including NTF2-Like SgcJ protein from Streptomyces carzinostaticus, which plays a role in the biosynthesis of the 9-membered enediyne antitumor antibiotic C-1027. It shows a cone-like alpha+beta barrel structure with a long N-terminal alpha- helix, a curved six-stranded antiparallel beta-sheet and two additional shorter alpha-helices. Its specific function is still unkown.
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 PF01218: Coproporphyrinogen III oxidase (family)
Coprogen oxidase (i.e. coproporphyrin III oxidase or coproporphyrinogenase) catalyses the oxidative decarboxylation of coproporphyrinogen III to proto-porhyrinogen IX in the haem and chlorophyll biosynthetic pathways . The protein is a homodimer containing two internally bound iron atoms per molecule of native protein . The enzyme is active in the presence of molecular oxygen that acts as an electron acceptor. The enzyme is widely distributed having been found in a variety of eukaryotic and prokaryotic sources.
Wikipedia: Coproporphyrinogen-III oxidase, mitochondrial is an enzyme that in humans is encoded by the CPOX gene. A genetic defect in the enzyme results in a reduced production of heme in animals. The medical condition associated with this enzyme defect is called hereditary coproporphyria.
Pfam PF21215: COP9 signalosome complex subunit 3-like, C-terminal helix (domain)
This domain is found in COP9 signalosome complex subunit 3 from humans (CSN3) and similar proteins predominantly found in vertebrates. CSN3 is a component of the eight-subunit COP9 signalosome complex (CSN), which inactivate Cullin-RING E3 ubiquitin ligases (CRLs) by removing their covalently attached activator, NEDD8. This entry represents the C-terminal helical decoration of this protein.
Pfam PF15766: Domain of unknown function (DUF4695) (family)
This family of proteins is found in eukaryotes. Proteins in this family are typically between 109 and 206 amino acids in length. There is a conserved RFKTQP sequence motif.
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 PF16308: Domain of unknown function (DUF4950) (family)
This family consists of several uncharacterized proteins around 250 residues in length and is mainly found in various Enterococcus faecalis species. The function of this family is unknown.
Pfam PF01526: Tn3 transposase DDE domain (domain)
This family includes transposases of Tn3, Tn21, Tn1721, Tn2501, Tn3926 transposons from E-coli.  The specific binding of the Tn3 transposase to DNA has been demonstrated. Sequence analysis has suggested that the invariant triad of Asp689, Asp765, Glu895 (numbering as in Tn3) may correspond to the D-D-35-E motif previously implicated in the catalysis of numerous transposases.
Pfam PF11406: Antimicrobial peptide tachystatin A (family)
Tachystatin A contains a cysteine-stabilised triple-stranded beta-sheet and shows features common to membrane-interactive peptides. Tachystatin A is thought to have an antimicrobial activity similar to defensins.Tachystatin A is also a chitin-binding peptide.
Pfam PF20602: Putative adhesive domain (group 8) (domain)
The structure model of this domain resembles the  C-terminal domains of the Streptococcus intermedius  antigen I/II (AgI/II). The N-terminal domain of AgI/II  (also called adhesin P1, antigen B or PAc) folds towards  the stalk, where it gets locked in place. Given that this domain  is found N-terminal to repeating stalk domains in bacterial  surface proteins, the domain is suggested to have a potential  protein binding function.
Pfam PF13082: Protein of unknown function (DUF3931) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 80 amino acids in length.
Pfam PF22476: Argonaute, N-terminal domain (domain)
This domain is found at the N-terminal end of Protein argonaute from Pyrococcus furiosus (Ago), a component of the RNAi effector complex (RISC). Ago is organised into four domains: N (this entry), PAZ ([pfam:PF12212]), middle and PIWI ([pfam:PF02171]). This domain shows a small four-stranded beta-sheet, three alpha-helices and a beta-hairpin.
Pfam PF06880: Protein of unknown function (DUF1262) (family)
This family represents a conserved region within a number of proteins of unknown function that seem to be specific to Arabidopsis thaliana. Note that some family members contain more than one copy of this region.
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 PF22832: PsaO transmembrane domain (domain)
PsaO is one of the nine membrane-embedded subunits of photosystem I. This entry represents the transmembrane domain that was shown to consists of three transmembrane helices arranged in an L-shape.
Pfam PF13775: Domain of unknown function (DUF4171) (domain)
This short family is frequently found at the N-terminus of Homeobox proteins.
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 PF03686: Uncharacterised protein family (UPF0146) (domain)
The function of this family of proteins is unknown.
Pfam PF03122: Herpes virus major capsid protein (family)
This family represents the major capsid protein (MCP) of herpes viruses. The capsid shell consists of 150 MCP hexamers and 12 MCP pentamers. One pentamer is found at each of the 12 apices of the icosahedral shell, and the hexamers form the edges and 20 faces.
Pfam PF14400: Inactive transglutaminase fused to 7 transmembrane helices (family)
A family of inactive transglutaminases fused to seven transmembrane  helices. The transglutaminase domain is predicted to be extracellularly  located. Members of this family are associated in gene neighbourhoods with a pepsin-like peptidase and an ATP-grasp of the RimK-family. The  ATP-grasp is predicted to modify the 7TM protein or a cofactor that  interacts with it.
Pfam PF10157: BLOC-1-related complex sub-unit 6 C-terminal helix (family)
This is a family of conserved proteins found from nematodes to humans.  Family members include BORCS6 (BLOC-1-related complex sub-unit 6) also known as Lyspersin (lysosome-dispersing protein) or C17orf59. It constitutes sub-unit 6 of the BORC complex (BLOC-one-related complex). BORC is a multisubunit complex that regulates the positioning of lysosomes at the cell periphery, and consequently affects cell migration. BORC associates with the lysosomal membrane, where it functions to recruit the small GTPase Arl8. This initiates a series of interactions that promote the microtubule-guided transport of lysosomes toward the cell periphery. this entry represents a C-terminal alpha helix according to structure predictions.
Pfam PF23705: RxLR effector (family)
This protein family includes a group of short sequences from lower eukaryotes, including RxLR effector protein from Phytophthora pseudosyringae.
Pfam PF23175: Stimulated by retinoic acid gene 8 protein bHLH domain (domain)
This bHLH domain is found in the family of Stimulated by retinoic acid gene 8 protein (STRA8). This protein is required for the transition into meiosis for both female and male germ cells. In female germ cells, it acts as a key effector of the meiotic program and is required for premeiotic DNA replication and subsequent events in meiotic prophase.
Pfam PF04858: TH1 protein (family)
TH1 is a highly conserved but uncharacterised metazoan protein. No homologue has been identified in Caenorhabditis elegans. TH1 binds specifically to A-Raf kinase.
Pfam PF11175: Protein of unknown function (DUF2961) (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.