SII-SWORD/CoKE huggingface dataset:
Pfam PF05036: SPOR domain (domain)
Bacterial SPOR domains bind peptidoglycan (PG) and target proteins to the cell division site by binding to denuded glycan strands that lack stem peptides.  This 70 residue domain is composed of two 35 residue repeats found in proteins involved in sporulation and cell division such as FtsN, DedD, and CwlM. This domain is involved in binding peptidoglycan. Two tandem repeats fold into a pseudo-2-fold symmetric single-domain structure containing numerous contacts between the repeats. FtsN is an essential cell division protein with a simple bitopic topology, a short N-terminal cytoplasmic segment fused to a large carboxy periplasmic domain through a single transmembrane domain. These repeats lay at the periplasmic C-terminus. FtsN localises to the septum ring complex.
Pfam PF18066: Phage ABA sandwich domain (domain)
This domain is found in a prophage protein BC1872 found in B. cereus. The domain forms a three-layer beta/alpha/beta sandwich. Three alpha-helices, alpha1, alpha2, and alpha3, are sandwiched on one side by three-stranded antiparallel beta-sheet (beta3, beta4, and beta5) and on the other by a beta-hairpin (beta1 and beta2).
Pfam PF03815: LCCL domain (domain)
The LCCL domain has been named after the best characterised proteins that were found to contain it, namely Limulus factor C, Coch-5b2 and Lgl1. It is an about 100 amino acids domain whose C-terminal part contains a highly conserved histidine in a conserved motif YxxxSxxCxAAVHxGVI. The LCCL module is thought to be an autonomously folding domain that has been used for the construction of various modular proteins through exon-shuffling. It has been found in various metazoan proteins in association with complement B-type domains, C-type lectin domains, von Willebrand type A domains, CUB domains, discoidin lectin domains or CAP domains. It has been proposed that the LCCL domain could be involved in lipopolysaccharide (LPS) binding . Secondary structure prediction suggests that the LCCL domain contains six Î² strands and two Î± helices . The structure of the LCCL domain from human Coch-5b2 has been solved. It has an unusual fold, where a centrally located helix is wrapped by extended polypeptide segments of mostly irregular secondary structure .

Some proteins known to contain a LCCL domain include Limulus factor C, a LPS endotoxin-sensitive trypsin type serine protease which serves to protect the organism from bacterial infection; vertebrate cochlear protein cochlin or coch-5b2 (Cochlin is probably a secreted protein, mutations affecting the LCCL domain of coch-5b2 cause the deafness disorder DFNA9 in humans); and mammalian late gestation lung protein Lgl1, contains two tandem copies of the LCCL domain .
Wikipedia: In molecular biology, the LCCL domain is a protein domain which has been named after several well-characterised proteins that were found to contain it, namely Limulus clotting factor C, Cochlin (Coch-5b2) and Lgl1 (CRISPLD2). It is an about 100 amino acids domain whose C-terminal part contains a highly conserved histidine in a conserved motif YxxxSxxCxAAVHxGVI. The LCCL module is thought to be an autonomously folding domain that has been used for the construction of various modular proteins through exon-shuffling. It has been found in various metazoan proteins in association with complement B-type domains, C-type lectin domains, von Willebrand type A domains, CUB domains, discoidin lectin domains or CAP domains. It has been proposed that the LCCL domain could be involved in lipopolysaccharide (LPS) binding. LCCL exhibits a novel fold.
Pfam PF05104: Ribosome receptor lysine/proline rich region (family)
This highly conserved region is found towards the C-terminus of the transmembrane domain. The function is unclear.
Pfam PF17221: COMMD1 N-terminal domain (domain)
This helical domain is found at the N-terminus of COMMD1.
Pfam PF17753: Ig-fold domain (domain)
This Ig-like fold domain is found in mannosidase enzymes.
Pfam PF24764: Integrase core domain (domain)
This domain is homologous to the integrase central catalytic domain.
Pfam PF04659: Archaeal flagella protein (family)
Family of archaeal flaD and flaE proteins.  Conserved region found at N-terminus of flaE but towards the C-terminus of flaD.
Pfam PF20788: YuA phage, Gp49 (family)
This domain family includes proteins from tailed bacteriophages such as Pseudomonas phage YuA. Gp49 shows an alpha-beta fold. Its function is unknown.
Pfam PF03193: RsgA GTPase (domain)
RsgA (also known as EngC and YjeQ) represents a protein family whose members are broadly conserved in bacteria and are indispensable for growth. The GTPase domain of RsgA is very similar to several P-loop GTPases, but differs in having a circular permutation of the GTPase structure described by a G4-G1-G3 pattern.
Pfam PF18005: eIF3 subunit M, C-terminal helix (domain)
This is the C-terminal helix domain found in Eukaryotic translation initiation factor 3 subunit M (eIF3m). In mammalian eIF3a, the C-terminal helix following the PCI domain is involved in interactions with other core subunits.
Pfam PF23865: Domain of unknown function (DUF7223) (domain)
This domain is found in uncharacterised proteins mainly from fungi. It is frequently found associated with ([pfam:PF22974]). This domain is predicted to adopt a globular structure with an elongated beta-sandwich topology.
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 PF24437: Integrator complex subunit 7 helical bundle (domain)
Integrator complex subunit 7 (INTS7) is a component of the integrator complex, a complex that is recruited to the U1 and U2 snRNA genes and mediates the snRNAs' 3' end processing. The integrator complex interacts with the C-terminal tail of the largest subunit of RNA-polymerase II to promote 3'-snRNA processing. This entry represents the helical bundle (HB) of INTS7, localised between the superhelical alpha-solenoid ([pfam:PF24436]) and the C-terminal beta- sandwich ([pfam:PF22965]). INTS7 interacts with INTS1 and INTS2 making extensive contacts with each other, nucleating the assembly of the whole INTAC complex.
Pfam PF24282: Family of unknown function (DUF7470) (family)
This family includes a group of short proteins from archaea. Members are predicted to adopt an alpha-helical structure.
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 PF15301: SLAIN motif-containing family (disordered)
The SLAIN motif containing family is named after the presence of a SLAIN motif in SLAIN1. They are a family of microtubule plus-end tracking proteins.
Pfam PF11703: UPF0506 (domain)
This uncharacterised family is found in Schistosoma genomes. Although uncharacterised it appears to belong to the knottin fold. The sequence is composed of two repeats of a 6 cysteine motif.
Pfam PF15705: TMEM132 N-terminal (domain)
This entry represents the N-terminal Ig-like domain found in TMEM132 family of proteins which includes TMEM132A-E, transmembrane proteins that regulate neuronal structure and function. In mammalian cells, they may regulate NAP1 in the WAVE regulatory complex (WRC) to finely modulate actin nucleation, cellular cytoskeletal and morphological changes. TMEM132D member has been associated with panic disorders, anxiety and major depressive disorders. This entry represents five of the seven beta-sheets as the last two are contributed by more distant residues in the sequence (i.e residues 647-677 in TMEM132A).
Pfam PF04984: Phage tail sheath protein subtilisin-like domain (domain)
This entry represents the second domain in a variety of phage tail sheath proteins. According to ECOD this domain has a subtilisin-like structure.
Pfam PF23406: ZNF380 coiled-coil (coiled_coil)
This entry represents a coiled-coil found at the C-terminal of Zinc finger protein 830 (also known as CCDC16 in humans), which may play a role in pre-mRNA splicing as component of the spliceosome. It is a component of the XAB2 complex, which binds RNA and a component of a pentameric intron-binding complex that is pre-assembled and then incorporated into the spliceosome. These proteins contain a zinc finger towards the N-terminal ([pfam:PF12874]).
Pfam PF16320: Ribosomal protein L7/L12 dimerisation domain (domain)
This is the N-terminal dimerisation domain of ribosomal protein L7/L12.
Pfam PF09521: NgoPII restriction endonuclease (family)
This family includes the NgoPII (recognises and cleaves GG^CC) restriction endonuclease.
Pfam PF16449: Fimbrillin MatB (domain)
This is a family of fimbrial proteins.
Pfam PF15096: G6b-B extracellular V-set Ig-like domain (domain)
G6b-B is a unique platelet ITIM-containing receptor that is highly expressed in mature megakaryocytes and platelets. t is a type I transmembrane protein that consists of a single N-glycosylated immunoglobulin-variable (IgV)-like domain in its extracellular region, a single transmembrane domain and a cytoplasmic tail containing an ITIM and an immunoreceptor tyrosine-based switch motif (ITSM). The extracellular matrix heparan sulfate (HS) proteoglycan perlecan was identified as a G6b-B binding partner. Subsequent in vitro biochemical studies and a cell-based genetic screen demonstrated that the interaction is specifically mediated by the HS chains of perlecan. This entry represents the N-terminal extracellular HS binding domain.
Wikipedia: Protein G6b is a protein that in humans is encoded by the G6B gene, or C6orf25.
Pfam PF05257: CHAP domain (domain)
This domain corresponds to an amidase function.  Many of these proteins are involved in cell wall metabolism of bacteria. This domain is found at the N-terminus of [swissprot:P43675], where it functions as a glutathionylspermidine amidase [ec:3.5.1.78]. This domain is found to be the catalytic domain of PlyCA. CHAP is the amidase domain of bifunctional Escherichia coli glutathionylspermidine synthetase/amidase, and it catalyses the hydrolysis of Gsp (glutathionylspermidine) into glutathione and spermidine.
Wikipedia: In molecular biology, the CHAP domain is a region between 110 and 140 amino acids that is found in proteins from bacteria, bacteriophages, archaea and eukaryotes of the family Trypanosomidae. The domain is named after the acronym cysteine, histidine-dependent amidohydrolases/peptidases. Many of these proteins are uncharacterised, but it has been proposed that they may function mainly in peptidoglycan hydrolysis. The CHAP domain is found in a wide range of protein architectures; it is commonly associated with bacterial type SH3 domains and with several families of amidase domains. It has been suggested that CHAP domain containing proteins utilise a catalytic cysteine residue in a nucleophilic-attack mechanism.
Pfam PF08171: Mad3/BUB1 homology region 2 (domain)
This domain is found in checkpoint proteins which are involved in cell division.  This region has been shown to be necessary and sufficient for the binding of MAD3 to BUB3 in Saccharomyces cerevisiae. This domain is present in BUB1 which also binds BUB3.
Pfam PF12510: Smoothelin cytoskeleton protein (family)
This domain family is found in eukaryotes, and is approximately 50 amino acids in length. The family is found in association with [pfam:PF00307]. Smoothelin is a cytoskeletal protein specifically expressed in differentiated smooth muscle cells and has been shown to co-localize with smooth muscle alpha actin.
Pfam PF19403: Prealbumin-like fold domain (domain)
Domain related to SpaA found as tandem repeats in bacterial surface proteins, associated with VWA and PA14 adhesins
Pfam PF06388: Protein of unknown function (DUF1075) (family)
This family consists of several eukaryotic 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 PF01814: Hemerythrin HHE cation binding domain (domain)
Iteration of the HHE family () found it to be related to Hemerythrin. It also demonstrated that what has been described as a single domain () in fact consists of two cation binding domains. Members of this family occur all across nature and are involved in a variety of processes. For instance, in Nereis diversicolor [swissprot:P80255] binds Cadmium so as to protect the organism from toxicity (). However Hemerythrin is classically described as Oxygen-binding through two attached Fe2+ ions. And the bacterial [swissprot:Q7WX96] is a regulator of response to NO, which suggests yet another set-up for its metal ligands (). In Staphylococcus aureus P72360 has been noted to be important when the organism switches to living in environments with low oxygen concentrations (); perhaps this protein acts as an oxygen store or scavenger. This domain can bind oxygen (Matilla et.al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043)
Wikipedia: Hemerythrin (also spelled haemerythrin; Ancient Greek: αἷμα, romanized: haîma, lit. 'blood', Ancient Greek: ἐρυθρός, romanized: erythrós, lit. 'red') is an oligomeric protein responsible for oxygen (O2) transport in the marine invertebrate phyla of sipunculids, priapulids, brachiopods, and in a single annelid worm genus, Magelona. Myohemerythrin is a monomeric O2-binding protein found in the muscles of marine invertebrates. Hemerythrin and myohemerythrin are essentially colorless when deoxygenated, but turn a violet-pink in the oxygenated state.
Pfam PF22433: Magnetotaxis protein MtxA, Immunoglobulin-like domain (domain)
This immunoglobulin-like domain is found in the Magnetotaxis protein MtxA from Magnetospirillum gryphiswaldense ([swissprot:A4TUL6]) and similar sequences from magnetotactic aquatic proteobacteria. Magnetotaxis is believed to direct the swimming of cells toward growth-favoring microoxic zones in natural waters.
Pfam PF16689: Coiled-coil N-terminus of APC, dimerisation domain (coiled_coil)
APC_N_CC is the N-terminal, coiled-coil dimerisation domain of the adenomatosis polyposis coli (APC) tumour-repressor proteins. It plays a key role in the regulation of cellular levels of the oncogene product beta-catenin. Coiled-coil regions are binding repeats that in this case bind to the armadillo repeat region of beta-catenin.
Pfam PF02870: 6-O-methylguanine DNA methyltransferase, ribonuclease-like domain (domain)
This entry represents the N-terminal ribonuclease-like domain associated with 6-O-methylguanine DNA methyltransferase activity. The repair of DNA containing O6-alkylated guanine is carried out by DNA-[protein]-cysteine S-methyltransferase (also known as O-6-methylguanine-DNA-alkyltransferase)
Pfam PF05761: 5' nucleotidase family (family)
This family of eukaryotic proteins includes 5' nucleotidase enzymes, such as purine 5'-nucleotidase [ec:3.1.3.5].
Pfam PF05559: Protein of unknown function (DUF763) (family)
This family consists of several uncharacterised bacterial and 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 PF10949: Protein of unknown function (DUF2777) (family)
This family of proteins with unknown function appears to be restricted to Bacillus cereus.
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 PF00560: Leucine Rich Repeat (repeat)
CAUTION: This Pfam may not find all Leucine Rich Repeats in a protein.  Leucine Rich Repeats are short sequence motifs present in a number of proteins with diverse functions and cellular locations.  These repeats are usually involved in protein-protein interactions. Each Leucine Rich Repeat is composed of a beta-alpha unit. These units form elongated non-globular structures. Leucine Rich Repeats are often flanked by cysteine rich domains.
Wikipedia: A leucine-rich repeat (LRR) is a protein structural motif that forms an α/β horseshoe fold. It is composed of repeating 20–30 amino acid stretches that are unusually rich in the hydrophobic amino acid leucine. These tandem repeats commonly fold together to form a solenoid protein domain, termed leucine-rich repeat domain. Typically, each repeat unit has beta strand-turn-alpha helix structure, and the assembled domain, composed of many such repeats, has a horseshoe shape with an interior parallel beta sheet and an exterior array of helices. One face of the beta sheet and one side of the helix array are exposed to solvent and are therefore dominated by hydrophilic residues. The region between the helices and sheets is the protein's hydrophobic core and is tightly sterically packed with leucine residues.
Pfam PF13812: Pentatricopeptide repeat domain (repeat)
This family matches additional variants of the PPR repeat that were not captured by the model for [pfam:PF01535]. In the case of the Arabidopsis protein UniProtKB:Q66GI4, the repeated helices in this N-terminal region, of protein-only RNase P (PRORP) enzymes, form the pentatricopeptide repeat (PPR) domain which enhances pre-tRNA binding affinity. PROPRP enzymes process precursor tRNAs in human mitochondria and in all tRNA-using compartments of Arabidopsis thaliana.
Wikipedia: The pentatricopeptide repeat (PPR) is a 35-amino acid sequence motif. Pentatricopeptide-repeat-containing proteins are a family of proteins commonly found in the plant kingdom. They are distinguished by the presence of tandem degenerate PPR motifs and by the relative lack of introns in the genes coding for them.
Pfam PF10875: Protein of unknown function (DUF2670) (family)
This bacterial 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 PF23152: NAD-specific glutamate dehydrogenase, second domain (domain)
This domain is found in yeast NAD-specific glutamate dehydrogenase (GDH2) and related fungal proteins. GDH2 is involved in the degradation of glutamate to ammonia and alpha-ketoglutarate. This domain is predicted to adopt an alpha/beta globular structure with some similarity to the ACT* domains of the bacterial large glutamate dehydrogenase and it is probably distantly related to these and other ACT-like domains.
Pfam PF22117: NADH-quinone oxidoreductase subunit 3, ferredoxin-like domain (domain)
NADH-quinone oxidoreductase subunit 3 (Nqo3) is a component of respiratory complex I. This protein is located at the peripheral arm of the complex and consists of multiple domains. This entry represents the second ferredoxin-like domain which contains Fe4-S4 cluster, one of the redox centers of the complex.
Pfam PF04682: Herpesvirus BTRF1 protein conserved region (family)
Herpesvirus protein.
Pfam PF18159: SMODS-associating 4TM effector domain (domain)
Predicted pore-forming effector domain found in conserved genome contexts with diverse nucleotide synthetases including the SMODS synthetases. Predicted to function as a pore-forming effector in a class of conflict systems reliant on the production of second messenger nucleotide or nucleotide derivatives. S-4TM domains are predicted to initiate cell suicide responses upon their activation.
Pfam PF23904: Domain of unknown function (DUF7246) (domain)
This entry describes a domain of unknown function found in phage proteins. The proteins containing this domain average 90 to 100 amino acids in length and is found in a variety of phage proteins, particularly those from Streptomyces and Mycobacterium phages. The domain usually occurs near the middle or C-terminus of proteins. The domain forms a small beta barrel.
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 PF24524: Domain of unknown function (DUF7596) (domain)
This is a GNAT-like domain found at the N-terminal of uncharacterised sequences from nematodes.
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 PF18624: CDI immunity protein (domain)
Contact-dependent growth inhibition (CDI) is a mechanism of inter-cellular competition in which Gram-negative bacteria exchange polymorphic toxins using type V secretion systems. Structure analysis of the CDI toxin from Escherichia coli NC101 reveals that it has moderate structural homology to Whirly-like proteins found in plastids, but appears to lack the characteristic Whirly RNA-binding site.
Pfam PF08135: Major transforming protein E5 family (family)
This family consists of the major transforming proteins (E5)  of the bovine papilloma virus (BPV). The equine sarcoid is  one of the most common dermatological lesion in equids. It is  a benign, locally invasive dermal fibroblastic lesion and  studies have shown an association of the lesions with BPV. E5  is a short hydrophobic membrane protein localising to the Golgi apparatus and other intracellular membranes. It binds to and constitutively activates the platelet-derived growth factor-beta in transformed cells. This stimulation activates a receptor signaling cascade which results in an intracellular growth stimulatory signal.
Pfam PF24531: Nuclear anchorage protein 1, spectrin repeat (domain)
This entry represents spectrin repeats found in Nuclear anchorage protein 1 from C. elegans, a protein that plays a central role in nuclear and mitochondrial anchoring. It may connect nuclei to the cytoskeleton by interacting with unc-84 at the nuclear envelope and with F-actin in the cytoplasm, creating a bridge across the nuclear envelope between the cytoskeleton and the nucleus.