SII-SWORD/CoKE huggingface dataset:
AMIN-like domain (AMIN-like)
Type: Domain

This domain is found in a group of extracellular likely lipoproteins that adopt a structure similar to the AMIN domain. However, there are some topological differences between the two domains. Members of this entry are predominantly found in actinomycetes.
Lipase-like, C-terminal domain (Lip-like_C)
Type: Domain

This domain is found in lipases from Staphylococcus hyicus (Lip) and related proteins. Lip has a broad substrate specificity hydrolysing a variety of triglycerides and phosphatidylcholines . This domain is also found in uncharacterised sequences from plants, fungi and a few sequences from Platyhelminthes. It adopts a fold typical for α/β hydrolases.
CFAP65, tenth Ig-like domain (Ig_CFAP65_10th)
Type: Domain

This entry represents the tenth Ig-like domain located towards the C-terminal in human Cilia- and flagella-associated protein 65 (CFAP65) and similar animal sequences.

Cilia-Flagella-Associated Protein 65 (CFAP65) is involved in the structural and functional integrity of cilia and flagella. This protein is implicated in the process of flagellar formation and is essential for proper sperm motility, suggesting a role in reproductive biology. CFAP65's function in flagellar assembly indicates its importance in the motility and sensory functions of cilia and flagella across different species .
CFAP74, second Ig-like domain (Ig-CFAP74_2nd)
Type: Domain

This entry represents the second Ig-like domain of CFAP74, a protein that is part of the central apparatus of the cilium axoneme and may play a role in cilium movement. It may play an important role in sperm architecture and function . Members of this entry are specific to animals.
CFAP74, third Ig-like domain (Ig-CFAP74_3rd)
Type: Domain

This entry represents the third Ig-like domain of CFAP74, a protein that is part of the central apparatus of the cilium axoneme and may play a role in cilium movement. It may play an important role in sperm architecture and function . Members of this entry are found in eukaryotes.
Anti-Pycsar protein Apyc1 (Anti-Pycsar_Apyc1)
Type: Family

This entry represents Anti-Pycsar protein Apyc1 from Bacillus phage SBSphiJ and similar sequences from tailed bacteriophages and bacterial prophages. Apyc1 counteracts the endogenous Pycsar antiviral defence system . Members of this group are phosphodiesterases that enable metal-dependent hydrolysis of host cyclic nucleotide Pycsar defence signals such as cCMP and cUMP . These proteins have a metallo beta-lactamase (MBL)-like fold with homology to RNase and phosphodiesterase enzymes .
CGL160/ATPI domain (CGL160/ATPI_dom)
Type: Domain

This domain is found in Protein CONSERVED ONLY IN THE GREEN LINEAGE 160 from Arabidopsis thaliana (CGL160), ATP synthase protein I (ATPI) from cyanobacteria and similar proteins. CGL160 facilitates the assembly of the membrane proton channel of the chloroplastic F-type ATPase . ATPI may guide the assembly of the membrane sector of the ATPase enzyme complex.
CFAP74, fourth Ig-like domain (Ig-CFAP74_4th)
Type: Domain

This entry represents the fourth Ig-like domain of CFAP74, a protein that is part of the central apparatus of the cilium axoneme and may play a role in cilium movement. It may play an important role in sperm architecture and function . Members of this entry are found in eukaryotes.
TMEM131, second Ig-like domain (TMEM131_Ig_2)
Type: Domain

This entry represents the second Ig-like domain from TMEM131.

TMEM131 is a collagen binding transmembrane protein involved in collagen secretion by recruiting the ER-to-Golgi transport complex TRAPPIII . Human TMEM131 is predicted to contain eight Ig-like domains.
Antitoxin Xre/MbcA/ParS-like, middle domain (Xre-MbcA-ParS_M)
Type: Domain

This entry represents a small domain found in the middle region of a group of uncharacterised bacterial sequences related to the antitoxin components of a type II toxin-antitoxin (TA) system Xre/MbcA/ParS. This domain may consist of four β-sheets and two short α-helices, which is followed by a toxin-binding domain (

).
Antitoxin Xre/MbcA/ParS-like, N-terminal (Xre_MbcA_ParS-like_N)
Type: Domain

This entry represents the N-terminal domain of a group of bacterial sequences related to the antitoxin components of a type II toxin-antitoxin (TA) system Xre/MbcA/ParS. This domain may adopt an α-helical fold.
AP-3 complex subunit beta-1/2, C-terminal domain (AP3B1/2_C)
Type: Domain

This domain is found at the C-terminal end of human AP-3 complex subunit beta-1/2 (AP3B1/2) and similar proteins from animals and plants. AP3B1 is a subunit of non-clathrin- and clathrin-associated AP-3 complex, which plays a role in protein sorting in the late-Golgi/trans-Golgi network (TGN) and/or endosomes . This domain is predicted to adopt a structure consisting of a five stranded β-sheet, flanked by one-α helix on the outer side, and by two α-helices on the inner side.
SmORF-like domain, apicomplexa (SmORF-like_dom_apicomplexa)
Type: Domain

This domain is found in a group of uncharacterised small proteins from apicomplexa, including SmORF (

) from the parasite Babesia bovis, which is encoded by an small open reading frame (smORF) . This domain, predicted to adopt an α-helical structure, is found twice in some longer members.
Microprotein, apicomplexa 2 (Microp_apicomplexa_2)
Type: Family

This protein family includes uncharacterised microproteins encoded by small open reading frames (smORFs) from apicomplexa, including

from the parasite Babesia bovis .
Microprotein, apicomplexa (Microp_apicomplexa)
Type: Family

This protein family includes uncharacterised microproteins encoded by small open reading frames (smORFs) from apicomplexa, including

from the parasite Babesia bovis .
Microprotein, apicomplexa 3 (Microp_apicomplexa_3)
Type: Family

This protein family includes uncharacterised microproteins encoded by small open reading frames (smORFs) from apicomplexa, including

from the parasite Babesia bovis .
NOMO, seventh transthyretin-like domain (NOMO_7th)
Type: Domain

This entry represents a domain centrally located in BOS complex subunit NOMO1-3 from vertebrates.

This domain is also found in the homologue Nicotinic receptor-associated protein 4 from Caenorhabditis elegans .

NOMO family of proteins includes NOMO1, NOMO2, NOMO3. These proteins are components of the multi-pass translocon (MPT) complex that mediates insertion of multi-pass membrane proteins into the lipid bilayer of membranes . They play an important role in the protein topogenesis and cells lacking these components show reduced multipass protein stability . NOMO proteins are multidomain proteins.
Microprotein, apicomplexa 4 (Microp_apicomplexa_4)
Type: Family

This protein family includes uncharacterised microproteins encoded by small open reading frames (smORFs) from apicomplexa, including

from the parasite Babesia bovis .
Microprotein domain, apicomplexa (Microp_dom_apicomplexa)
Type: Domain

This domain covers the whole length of uncharacterised microproteins encoded by small open reading frames (smORFs) from apicomplexa, including

from the parasite Babesia bovis , and is found at the N-terminal end of longer uncharacterised proteins from related species.
Microprotein, apicomplexa 21 (Microp_apicomplexa_21)
Type: Family

This protein family includes uncharacterised microproteins encoded by small open reading frames (smORFs) from apicomplexa, including

from the parasite Babesia bovis .
Microprotein domain, apicomplexa 2 (Microp_dom_apicomplexa_2)
Type: Domain

This domain covers the whole length of uncharacterised microproteins encoded by small open reading frames (smORFs) from apicomplexa, including

from the parasite Babesia bovis , and is found centrally located in longer uncharacterised proteins from related species.
Microprotein domain, apicomplexa 19 (Microp_apicomplexa_19)
Type: Domain

This domain is found in uncharacterised microproteins encoded by small open reading frames (smORFs) from apicomplexa, including

from the parasite Babesia bovis .
Microprotein, apicomplexa 18 (Microp_apicomplexa_18)
Type: Family

This protein family includes uncharacterised microproteins encoded by small open reading frames (smORFs) from apicomplexa, including

from the parasite Babesia bovis .
Microprotein, apicomplexa 7 (Microp_apicomplexa_7)
Type: Family

This protein family includes uncharacterised microproteins encoded by small open reading frames (smORFs) from apicomplexa, including

from the parasite Babesia bovis .
ARMC9, CTLH-like domain (ARMC9_CTLH-like_dom)
Type: Domain

This entry represents a domain that is found C-terminal to LisH motif in human LisH domain-containing protein ARMC9 and related proteins. Armc9 is involved in ciliogenesis and is required for appropriate acetylation and polyglutamylation of ciliary microtubules, and regulation of cilium length . This domain is distantly related to the CTLH/CRA domain (

) found in proteins components of ubiquitin-protein ligase complex.

This domain is found also in Suppressor of organelle fusion 1 from Caenorhabditis elegans and vertebrate WD repeat-containing protein 91 both acting as negative regulators of the PI3 kinase/PI3K activity associated with endosomal membranes .
ATP-dependent RNA helicase DHX29, DSRM-like domain (DSRM_DHX29)
Type: Domain

This is a presumed domain found near the middle of ATP-dependent RNA helicase DHX29 from human and at the N-terminal of the putative ATP-dependent RNA helicase YLR419W from yeast, which has been identified as the homologue of the translation initiation factor DHX29 from human . DHX29 is a DExH-box protein involved in eukaryotic translation initiation. DHX29 is required to bind to the 40S subunit of the 43S preinitiation complex to allow highly structured 5'-UTRs to be scanned . This domain is similar to DSRM (Double-Stranded RNA-binding Motif, also known as dsRBD) domains.
ATP-dependent RNA helicase HrpB, connector region (CON_HrpB)
Type: Domain

This domain is found in ATP-dependent RNA helicase HrpB from Escherichia coli and similar proteins predominantly found in proteobacteria. It is a connector element (CON) found N-terminal to

.

The DExH-box group of NTPases/helicases in bacteria predominantly comprises DEAH/RHA-like proteins and it was divided into three groups: HrpA-like, HrpB-like, and Z5898-like proteins, referring to three corresponding E.coli factors . While motifs II of HrpA- and Z5898-like proteins conform to the DEAH fingerprint of DEAH/RHA enzymes, motif II of HrpB-like helicases comprises the sequence Asp-Glu-Phe/Tyr-His, which is more closely related to the corresponding motif in Ski2-like enzymes.
ATP-dependent rRNA helicase SPB4-like, C-terminal tail (CTT_SPB4)
Type: Domain

This domain is found at the C-terminal end of ATP-dependent rRNA helicase SPB4 from Saccharomyces cerevisiae and similar sequences mainly from fungi and some animal species. SPB4 is involved in the biogenesis of 60S ribosomal subunits. It is is organised into four domains: dual RecA domains (

and

), a C-terminal extension (

) and a C-terminal tail (CTT, this entry). This domain forms a V-shaped α-helical structure .
BBS7, beta-propeller (Beta-prop_BBS7)
Type: Domain

This entry represents the BBS7 β-propeller domain. The BBS7 β-propeller interacts with the β-propeller domain of another BBSome protein, BBS1, in order to control access of the membrane-recruiting protein ARL6 . Members of this group are mainly found in animals.

Bardet-Biedl syndrome 7 (BBS7) forms a part of the BBSome complex, which is required for ciliogenesis . BBS7 is the BBSome subunit responsible for the binding to SMO H8 and plays a role in guanylyl cyclase localisation in the ring-like structures at the base of the finger compartment in AFD sensory neurons . BBS7 and BBS2 form the head of the BBSome via an asymmetric heterodimer formation . BBS2, BBS7, and BBS9 share the same five-domain architecture with an N-terminal β-propeller followed by a heterodimerization α-helix, an immunoglobulin-like GAE domain (GAE), a mixed α/β plaform domain, and an α-helical region composed on two distinct helical hairpins.

Bardet-Biedl syndrome is a member of genetic ciliopathies, but the link between cilia/centrosome deficits and metabolic abnormalities is not completely clear . Bardet-Biedl syndrome (BBS) is a heterogeneous genetic disorder characterised by many features, including retinal degeneration, obesity, cognitive impairment, polydactyly, renal abnormalities, and hypogenitalism. BBS genes play an important role in maintaining leptin sensitivity in proopiomelanocortin neurons . A relatively high incidence of BBS is found in the mixed Arab populations of Kuwait and in Bedouin tribes throughout the Middle East, most likely due to the high rate of consaguinity in these populations and a founder effect.

Primary cilia are ubiquitous cellular appendages that provide important sensory and signalling functions and their dysfunction underlies numerous human genetic disorders. The proteins disrupted in the human ciliary disorder Bardet-Biedl syndrome (BBS) are required for the localisation of G protein-coupled receptors to primary cilia on central neurons. The alteration of signalling caused by mislocalisation of ciliary signalling proteins underlies the BBS phenotype . Of the 12 known BBS genes, BBS1 is the most commonly mutated .
BBS7, platform domain (BBS7_pf_dom)
Type: Domain

This entry represents the platform domain of BBS7. Members of this group are mainly found in animals.

Bardet-Biedl syndrome 7 (BBS7) forms a part of the BBSome complex, which is required for ciliogenesis . BBS7 is the BBSome subunit responsible for the binding to SMO H8 and plays a role in guanylyl cyclase localisation in the ring-like structures at the base of the finger compartment in AFD sensory neurons . BBS7 and BBS2 form the head of the BBSome via an asymmetric heterodimer formation . BBS2, BBS7, and BBS9 share the same five-domain architecture with an N-terminal β-propeller followed by a heterodimerization α-helix, an immunoglobulin-like GAE domain (GAE), a mixed α/β plaform domain, and an α-helical region composed on two distinct helical hairpins.

Bardet-Biedl syndrome is a member of genetic ciliopathies, but the link between cilia/centrosome deficits and metabolic abnormalities is not completely clear . Bardet-Biedl syndrome (BBS) is a heterogeneous genetic disorder characterised by many features, including retinal degeneration, obesity, cognitive impairment, polydactyly, renal abnormalities, and hypogenitalism. BBS genes play an important role in maintaining leptin sensitivity in proopiomelanocortin neurons . A relatively high incidence of BBS is found in the mixed Arab populations of Kuwait and in Bedouin tribes throughout the Middle East, most likely due to the high rate of consaguinity in these populations and a founder effect.

Primary cilia are ubiquitous cellular appendages that provide important sensory and signalling functions and their dysfunction underlies numerous human genetic disorders. The proteins disrupted in the human ciliary disorder Bardet-Biedl syndrome (BBS) are required for the localisation of G protein-coupled receptors to primary cilia on central neurons. The alteration of signalling caused by mislocalisation of ciliary signalling proteins underlies the BBS phenotype . Of the 12 known BBS genes, BBS1 is the most commonly mutated .
BBS7, GAE domain (BBS7_GAE_dom)
Type: Domain

This entry represents the gamma-adaptin ear (GAE) domain of BBS7. Members of this group are mainly found in animals.

Bardet-Biedl syndrome 7 (BBS7) forms a part of the BBSome complex, which is required for ciliogenesis . BBS7 is the BBSome subunit responsible for the binding to SMO H8 and plays a role in guanylyl cyclase localisation in the ring-like structures at the base of the finger compartment in AFD sensory neurons . BBS7 and BBS2 form the head of the BBSome via an asymmetric heterodimer formation . BBS2, BBS7, and BBS9 share the same five-domain architecture with an N-terminal β-propeller followed by a heterodimerization α-helix, an immunoglobulin-like GAE domain (GAE), a mixed α/β plaform domain, and an α-helical region composed on two distinct helical hairpins.

Bardet-Biedl syndrome is a member of genetic ciliopathies, but the link between cilia/centrosome deficits and metabolic abnormalities is not completely clear . Bardet-Biedl syndrome (BBS) is a heterogeneous genetic disorder characterised by many features, including retinal degeneration, obesity, cognitive impairment, polydactyly, renal abnormalities, and hypogenitalism. BBS genes play an important role in maintaining leptin sensitivity in proopiomelanocortin neurons . A relatively high incidence of BBS is found in the mixed Arab populations of Kuwait and in Bedouin tribes throughout the Middle East, most likely due to the high rate of consaguinity in these populations and a founder effect.

Primary cilia are ubiquitous cellular appendages that provide important sensory and signalling functions and their dysfunction underlies numerous human genetic disorders. The proteins disrupted in the human ciliary disorder Bardet-Biedl syndrome (BBS) are required for the localisation of G protein-coupled receptors to primary cilia on central neurons. The alteration of signalling caused by mislocalisation of ciliary signalling proteins underlies the BBS phenotype . Of the 12 known BBS genes, BBS1 is the most commonly mutated .
BBS7, helical hairpin (BBS7_hairpin)
Type: Domain

This entry represents a helical hairpin domain found in Bardet-Biedl syndrome 7 (BBS7) proteins from animals, including human and mouse.

Bardet-Biedl syndrome 7 (BBS7) forms a part of the BBSome complex, which is required for ciliogenesis . BBS7 is the BBSome subunit responsible for the binding to SMO H8 and plays a role in guanylyl cyclase localisation in the ring-like structures at the base of the finger compartment in AFD sensory neurons . BBS7 and BBS2 form the head of the BBSome via an asymmetric heterodimer formation . BBS2, BBS7, and BBS9 share the same five-domain architecture with an N-terminal β-propeller followed by a heterodimerization α-helix, an immunoglobulin-like GAE domain (GAE), a mixed α/β plaform domain, and an α-helical region composed on two distinct helical hairpins.

Bardet-Biedl syndrome is a member of genetic ciliopathies, but the link between cilia/centrosome deficits and metabolic abnormalities is not completely clear . Bardet-Biedl syndrome (BBS) is a heterogeneous genetic disorder characterised by many features, including retinal degeneration, obesity, cognitive impairment, polydactyly, renal abnormalities, and hypogenitalism. BBS genes play an important role in maintaining leptin sensitivity in proopiomelanocortin neurons . A relatively high incidence of BBS is found in the mixed Arab populations of Kuwait and in Bedouin tribes throughout the Middle East, most likely due to the high rate of consaguinity in these populations and a founder effect.

Primary cilia are ubiquitous cellular appendages that provide important sensory and signalling functions and their dysfunction underlies numerous human genetic disorders. The proteins disrupted in the human ciliary disorder Bardet-Biedl syndrome (BBS) are required for the localisation of G protein-coupled receptors to primary cilia on central neurons. The alteration of signalling caused by mislocalisation of ciliary signalling proteins underlies the BBS phenotype . Of the 12 known BBS genes, BBS1 is the most commonly mutated .
Calcium channel YVC1-like, C-terminal transmembrane domain (YVC1_C)
Type: Domain

This domain is found at the C-terminal of Calcium channel YVC1 from Saccharomyces cerevisiae, a transient receptor potential (TRP) channel required for release of calcium ions from the vacuole in response to hyperosmotic shock. This domain adopts an all-α configuration . It is often found associated with

. Members of this group are found in fungi.
YVC1, N-terminal linker helical domain (LHD_YVC1)
Type: Domain

This domain is found N-terminal in the yeast calcium channel YVC1 (also known as TRPY1) and similar fungal proteins. YVC1 is a transient receptor potential (TRP) channel that acts as a mechanosensitive osmoregulator. It is non-selective Ca2+ permeable and polymodal cation channel that function similarly to other TRP channels. YVC1 forms a domain-swapped homotetramer with each subunit composed of an N-terminal cytosolic linker helical domain (LHD, represented by this entry) and a transmembrane domain . The LHD domain is composed of eight closely packed α-helices and may harbour the docking site for binding partners in the cytosol .
Cap1-like, TM helices (Cap15-like_TM)
Type: Domain

This entry includes CD-NTase-associated protein 15 from Yersinia aleksiciae (Cap15,

), an effector protein of a CBASS antivirus system . These proteins occur in conserved genome contexts with the SMODS nucleotide synthetase . Cap15 consists of two transmembrane segments (TM) at the N-terminal, represented in this entry, and a compact eight-stranded β-barrel scaffold that forms a cyclic dinucleotide receptor domain (

) which oligomerises upon activation . Activated Cap15 binds the cyclic nucleotide second messenger 3',3'-cGAMP, relocalises throughout the cell and specifically induces rupture of the inner membrane.
Card1, CARF domain (CARF_Card1)
Type: Domain

This is the CARF domain found at the N-terminal of a set of bacterial proteins, including Card1 (cyclic-oligoadenylate-activated single-stranded ribonuclease and single-stranded deoxyribonuclease 1) from Treponema succinifaciens (

), a protein that is part of type III CRISPR-Cas immune response system. This protein consists of a CARF (CRISPR-associated Rossmann fold) domain at the N-terminal, an helical hinge domain and a C-terminal endonuclease domain (

) .
Carboxypeptidase Rv3627c-like, N-terminal domain (Rv3627c-like_N)
Type: Domain

This is the short N-terminal domain of Carboxypeptidase Rv3627c from Mycobacterium tuberculosis and similar sequences found in actinobacteria. This domain is predicted to form an α-helix.

Carboxypeptidase Rv3627c cleaves terminal D-alanine from peptidoglycan in the mycobacterial cell wall. It exerts important effects on mycobacterial cell morphology and cell division .
Chp1, domain II (Chp1_domII)
Type: Domain

Chp1 is required for RNA interference-dependent heterochromatin formation in fission yeast, and it is a member of the RNA-induced transcriptional silencing (RITS) complex which maintains the heterochromatin regions, playing a role in stabilising microtubules which allows accurate chromosome segregation .

This entry represents the second domain (domain II) of Chp1 which resembles eukaryotic phosphatases and receiver domains of bacterial phosphotransferase signalling systems, being part of the Rossmann fold superfamily. This domain makes the interaction surface between Chp1 and Tas3. Chp1 and Tas3 complex solid and versatile platform to recruit both RNAi-dependent and RNAi-independent gene-silencing pathways for locus-specific regulation of heterochromatin .
Chromodomain-helicase-DNA-binding protein 6-9, tri-helical domain (HTH_CHD6-9)
Type: Domain

This domain is found in human Chromodomain-helicase-DNA-binding proteins 6-9 (CHD6-9) which are DNA-dependent ATPases that play a role in chromatin remodelling and transcriptional regulation . CHD8 acts as a transcription repressor by remodelling chromatin structure and recruiting histone H1 to target genes. It suppresses p53/TP53-mediated apoptosis by recruiting histone H1 and preventing p53/TP53 transactivation activity. It also acts as a negative regulator of Wnt signalling pathway by regulating beta-catenin (CTNNB1) activity . CHD6 regulates transcription by disrupting nucleosomes in a largely non-sliding manner which strongly increases the accessibility of chromatin. It activates transcription of specific genes in response to oxidative stress through interaction with NFE2L2 . CHD9 acts as a transcriptional coactivator for PPARA and possibly other nuclear receptors .

This domain is predicted to form a tri-helical structure, with a three-membered α-helical bundle and a two-stranded antiparallel β-sheet. Members of this family are predominantly found in vertebrates.