SII-SWORD/CoKE huggingface dataset:
Domain of unknown function DUF7729 (DUF7729)
Type: Domain

This domain is found in uncharacterised fungal proteins. It is predicted to adopt a globular structure consisting of array of α-helices. It contains several conserved cysteine residues that are predicted to form disulfide bonds. It is likely that the proteins containing this domain are secreted.
NqrA, N-terminal barrel-sandwich hybrid domain (NQRA_N)
Type: Domain

This domain is found N-terminal in several bacterial Na(+)-translocating NADH-quinone reductase subunit A (NqrA) proteins. The Na(+)-translocating NADH: ubiquinone oxidoreductase (Na(+)-NQR) generates an electrochemical Na(+) potential driven by aerobic respiration . This domain has a significant similarity to known barrel-sandwich hybrid domains . It is often found associated with

and

.
NqrA, second alpha/beta domain (NQRA_2nd)
Type: Domain

This domain is found in several bacterial Na(+)-translocating NADH-quinone reductase subunit A (NqrA) proteins. The Na(+)-translocating NADH: ubiquinone oxidoreductase (Na(+)-NQR) generates an electrochemical Na(+) potential driven by aerobic respiration . This domain has an α/β structure and binds an FMN cofactor . It is often found associated with

and

.
ATP-dependent RNA helicase PRP5/DDX46/KHDC4, KH domain (PRP5/DDX46/KHDC4_KH)
Type: Domain

This entry represents a likely RNA-binding KH domain found at the C teminus of Pre-mRNA-processing ATP-dependent RNA helicase PRP5 from Saccharomyces cerevisiae, the Probable ATP-dependent RNA helicase DDX46 from human (DDX46) and similar eukaryotic proteins. PRP5 is involved in spliceosome assembly and in nuclear splicing . DDX46 is a component of the 17S U2 SnRNP complex of the spliceosome, a large ribonucleoprotein complex that removes introns from transcribed pre-mRNAs .

This domain is also found in the KH homology domain-containing protein 4 (KHDC4) which is an RNA-binding protein involved in pre-mRNA splicing via its interaction with the PRP19C/Prp19 complex/NTC/Nineteen complex .
CDC20/Fizzy, WD40 domain (WD40_CDC20-Fz)
Type: Domain

This entry represents the β-propeller found in the homologues of WD40 protein Cdc20/Fizzy, a protein that associates and phosphorylates anaphase promoting complex/cyclosome (APC/C) at the end of mitosis . It is required for full ubiquitin ligase activity of the APC/C and confers substrate specificity upon the complex .
DDB1- and CUL4-associated factor 12, beta-propeller domain (Beta-prop_DCAF12)
Type: Domain

This entry represents the β-propeller domain found in DDB1- and CUL4-associated factor 12 proteins (DCAF12) as well as DCAF12-like proteins 1 and 2 (DCAF12L1 and DCAF12L2) from animals. DCAF proteins have been hypothesised to play important roles during spermatogenesis due to their high level of conservation in mammals and testis enrichment . Mutations in DCAF12L1 has only been associated to male infertility in humans but not in mice . In insects, mutations in the DCAF12 homolog impairs larval development . The function of this domain is unknown.
IFT122, second beta-propeller domain (Beta-prop_IFT122_2nd)
Type: Domain

This entry represents the second β-propeller of IFT122, which is a crucial subunit for IFT-A integrity .

Intraflagellar transport protein 122 homolog IFT122 is one of the core components (together with WDR19/IFT144 and IFT140) of the IFT-A complex which is required for retrograde ciliary transport and entry into cilia of G protein-coupled receptors (GPCRs), being involved in cilia function and/or assembly . IFT-A polymerises interacts with IFT-B, and uses an array of β-propeller and TPR domains to create 'carriages' of the IFT train that engage TULP adaptor proteins .
IFT122, first beta-propeller domain (Beta-prop_IFT122_1st)
Type: Domain

This entry represents the first β-propeller of IFT122, which is a crucial subunit for IFT-A integrity .

Intraflagellar transport protein 122 homolog IFT122 is one of the core components (together with WDR19/IFT144 and IFT140) of the IFT-A complex which is required for retrograde ciliary transport and entry into cilia of G protein-coupled receptors (GPCRs), being involved in cilia function and/or assembly . IFT-A polymerises interacts with IFT-B, and uses an array of β-propeller and TPR domains to create 'carriages' of the IFT train that engage TULP adaptor proteins .
IFT140, first beta-propeller domain (Beta-prop_IFT140_1st)
Type: Domain

This entry represents the first β-propeller of IFT140.

IFT140 is one of the core components (together with WDR19/IFT144 and IFT122) of the IFT-A complex which is required for retrograde ciliary transport and entry into cilia of G protein-coupled receptors (GPCRs), being involved in cilia function and/or assembly . IFT-A polymerises interacts with IFT-B, and uses an array of β-propeller and TPR domains to create 'carriages' of the IFT train that engage TULP adaptor proteins . The β-propeller domains of IFT140 contact the β-propeller domains of IFT121 from the adjacent complex .
IFT140, second beta-propeller domain (Beta-prop_IFT140_2nd)
Type: Domain

This entry represents the second β-propeller of IFT140.

IFT140 is one of the core components (together with WDR19/IFT144 and IFT122) of the IFT-A complex which is required for retrograde ciliary transport and entry into cilia of G protein-coupled receptors (GPCRs), being involved in cilia function and/or assembly . IFT-A polymerises interacts with IFT-B, and uses an array of β-propeller and TPR domains to create 'carriages' of the IFT train that engage TULP adaptor proteins . The β-propeller domains of IFT140 contact the β-propeller domains of IFT121 from the adjacent complex .
IF140, C-terminal TPR domain (TPR_IF140_C)
Type: Domain

This entry represents the TPR domain found at the C-terminal of IFT140.

IFT140 is one of the core components (together with WDR19/IFT144 and IFT122) of the IFT-A complex which is required for retrograde ciliary transport and entry into cilia of G protein-coupled receptors (GPCRs), being involved in cilia function and/or assembly . IFT-A polymerises interacts with IFT-B, and uses an array of β-propeller and TPR domains to create 'carriages' of the IFT train that engage TULP adaptor proteins . The β-propeller domains of IFT140 contact the β-propeller domains of IFT121 from the adjacent complex .
IFT80/172/WDR35, TPR domain (TPR_IFT80_172_dom)
Type: Domain

This entry represents the tetratricopeptide-like repeats (TPRs) domain found in proteins comprising the intraflagellar transport (IFT) complexes B2 and A, which are found in nematodes and mammals, including IFT80, IF172, WDR35, DYF2 and other eukaryotic proteins. The IFT complex is required for retrograde ciliary transport and entry of G protein-coupled receptors (GPCRs) into cilia, and it is involved in ciliogenesis .
IFT121, second beta-propeller domain (Beta-prop_IFT121_2nd)
Type: Domain

This entry represents the second β-propeller of IFT121.

IFT121 (also known as WDR35) is a component of the IFT complex A (IFT-A), which is required for retrograde ciliary transport and entry into cilia of G protein-coupled receptors that is involved in ciliogenesis and ciliary protein trafficking . This protein plays a role in cilia assembly and maintenance . IFT121 contains a zinc finger with rubredoxin-like fold . Knock-out IFT121 cells showed defective retrograde trafficking within cilia .
IFT121/TULP4, N-terminal (Beta-prop_IFT121_TULP_N)
Type: Domain

This entry represents a β-propeller domain found at the N-terminal of IFT121 (which corresponds to the first one) and TULP4 proteins. TULP4 may be a substrate-recognition component of a SCF-like ECS (Elongin-Cullin-SOCS-box protein) E3 ubiquitin ligase complex. IFT-A polymerises and interacts with IFT-B, and uses an array of β-propeller and TPR domains to create 'carriages' of the IFT train that engage TULP adaptor proteins . Proteins in this entry are part of the non-core subcomplex, together with IFT43 and IFT139 .

IFT121 (also known as WDR35) is a component of the IFT complex A (IFT-A), which is required for retrograde ciliary transport and entry into cilia of G protein-coupled receptors that is involved in ciliogenesis and ciliary protein trafficking . This protein plays a role in cilia assembly and maintenance . IFT121 contains a zinc finger with rubredoxin-like fold . Knock-out IFT121 cells showed defective retrograde trafficking within cilia .
Leucine-rich repeat and WD repeat-containing protein 1, WD domain (WD_LRWD1)
Type: Domain

This entry represents the WD (β-propeller) domain found at the C-terminal of Leucine-rich repeat and WD repeat-containing protein 1 (LRWD1) from animals and related sequences. This domain is required for chromatin association of LRWD1 and for its binding to ORC .

LRWD1 (also known as CENP-33 and ORCA) is required for for G1/S transition. It recruits and stabilises the origin recognition complex (ORC) onto chromatin during G1 to establish pre-replication complex (preRC) and to heterochromatic sites in pre-replicated cells . This proteins consist of a LRR domain at the N terminus and a WD domain at the C terminus.
MABP1/WDR62, first WD40 domain (WD40_MABP1-WDR62_1st)
Type: Domain

This entry represents the first WD40 domain of MABP1 and WDR62.

MABP1 (Mitogen-activated protein kinase-binding protein 1) is a negative regulator of NOD2 function, leading to the down-regulation of NOD2-induced processes such as activation of NF-kappa-B signalling, IL8 secretion and antibacterial response . WDR62 is a microcephaly-related, microtubule (MT)-associated protein (MAP) that localises to the spindle pole and regulates spindle organisation by recruiting katanin to the spindle pole by forming a complex with TPX2/Aurora A . The microtubule-binding (MT) affinity of WDR62 is autoinhibited through JNK phosphorylation-induced intramolecular interaction . Additionally, WRD62 is implicated in the development of the cerebral cortex influencing both the proliferation and migration of neurons . The WD40 domains of WDR62 mediate the interaction with Aurora A and (MT binding) .
MABP1/WDR62, second WD40 domain (WD40_MABP1-WDR62_2nd)
Type: Domain

This entry represents the second WD40 domain of MABP1 and WDR62.

MABP1 (Mitogen-activated protein kinase-binding protein 1) is a negative regulator of NOD2 function, leading to the down-regulation of NOD2-induced processes such as activation of NF-kappa-B signalling, IL8 secretion and antibacterial response . WDR62 is a microcephaly-related, microtubule (MT)-associated protein (MAP) that localises to the spindle pole and regulates spindle organisation by recruiting katanin to the spindle pole by forming a complex with TPX2/Aurora A . The microtubule-binding (MT) affinity of WDR62 is autoinhibited through JNK phosphorylation-induced intramolecular interaction . Additionally, WRD62 is implicated in the development of the cerebral cortex influencing both the proliferation and migration of neurons . The WD40 domains of WDR62 mediate the interaction with Aurora A and (MT binding) .
Transcriptional regulator TbsP-like, C-terminal domain (TbsP_C)
Type: Domain

This domain is found at the C terminus of the putative transcriptional regulator TbsP from Haloferax volcanii (Halobacterium volcanii) (

, also known as HVO_2861) and similar sequences predominantly found in Halobacteria. TbsP is required for adhesion to abiotic surfaces (i.e., biofilm formation) and maintains wild-type cell morphology and motility. This domain is predicted to adopt a MarR-type helix-turn-helix (HTH) structure .
ELP1, first N-terminal beta-propeller (Beta-prop_ELP1_1st)
Type: Domain

This entry represents the first out of two N-terminal β-propeller domains, found in Elongator complex protein 1 (ELP1) from eukaryotes.

Elongator is a conserved protein complex implicated in multiple processes including regulation of transcription, alpha-tubulin acetylation, and tRNA modification. Mutations in the ELP1 gene have been shown to cause the neurodegenerative disease familial dysautonomia . ELP1 binds members of the Elongator complex ELP2 and ELP3; and the β-propellers are suggested to act as scaffold for this protein-protein interaction . Also known as IKAP, ELP1 acts as a regulator of IkB kinase complex involved in proinflammatory cytokine signalling. Residues within the central β-propeller have been shown to be required for interaction with upstream regulatory kinase NIK, acting as a scaffold that assembles IKKs with NIK .
ELP1, N-terminal second beta-propeller (Beta-prop_ELP1_2nd)
Type: Domain

This entry represents second out of two N-terminal β-propeller domains, found in Elongator complex protein 1 (ELP1) from eukaryotes.

Elongator is a conserved protein complex implicated in multiple processes including regulation of transcription, alpha-tubulin acetylation, and tRNA modification. Mutations in the ELP1 gene have been shown to cause the neurodegenerative disease familial dysautonomia . ELP1 binds members of the Elongator complex ELP2 and ELP3; and the β-propellers are suggested to act as scaffold for this protein-protein interaction . Also known as IKAP, ELP1 acts as a regulator of IkB kinase complex involved in proinflammatory cytokine signalling. Residues within the central β-propeller have been shown to be required for interaction with upstream regulatory kinase NIK, acting as a scaffold that assembles IKKs with NIK .
ELP1, TPR domain (TPR_ELP1)
Type: Domain

This entry represents the TPR domain found within the C-terminal dimerisation domain of Elongator complex protein 1 (ELP1), from eukaryotes.

Elongator is a conserved protein complex implicated in multiple processes including regulation of transcription, alpha-tubulin acetylation and tRNA modification. Mutations in the ELP1 gene have been shown to cause the neurodegenerative disease familial dysautonomia . The C-terminal dimerisation domain consists of 28 α-helices organised in three domains: an elongated α-solenoid domain (helices 1 to 14); a TPR domain, formed by six double-helix repeats (helices 15 to 26); and a three-helix bundle, C-terminal cap (helices 26 to 28) . ELP1 self-association contributes to its stability and is important for Elongator assembly . ELP1 is considered to function both as a scaffold, for Elongator complex ELP2 and ELP3 binding, and as a docking site for various factors that regulate Elongator activity . Also known as IKAP, ELP1 acts as a regulator of IkB kinase complex involved in proinflammatory cytokine signalling .
ELP1, alpha-solenoid (A-sol_ELP1)
Type: Domain

This entry represents the α-solenoid domain found within the C-terminal dimerisation domain of Elongator complex protein 1 (ELP1) from eukaryotes. Residues within the α-14-helix are highly conserved from yeast to human and act as a kink to maintain the TPR-like domain and α-solenoid domain at nearly a 90-degree angle.

Elongator is a conserved protein complex implicated in multiple processes including regulation of transcription, alpha-tubulin acetylation and tRNA modification. Mutations in the ELP1 gene have been shown to cause the neurodegenerative disease familial dysautonomia . The C-terminal dimerisation domain consists of 28 α-helices organised in three domains: an elongated α-solenoid domain (helices 1 to 14); a TPR domain, formed by six double-helix repeats (helices 15 to 26); and a three-helix bundle, C-terminal cap (helices 26 to 28) . ELP1 self-association contributes to its stability and is important for Elongator assembly . ELP1 is considered to function both as a scaffold, for Elongator complex ELP2 and ELP3 binding, and as a docking site for various factors that regulate Elongator activity . Also known as IKAP, ELP1 acts as a regulator of IkB kinase complex involved in proinflammatory cytokine signalling .
IF140/IFT172/WDR19, TPR domain (TPR_IF140/IFT172/WDR19)
Type: Domain

This entry represents the TPR region of IFT140/IFT172/WDR19 and similar proteins. IFT172 is a component of the IFT-B complex which interacts with IFT-A complex. This domain of IFT140 forms an interface with IFT144 .

IFT140 is one of the core components (together with WDR19/IFT144 and IFT122) of the IFT-A complex which is required for retrograde ciliary transport and entry into cilia of G protein-coupled receptors (GPCRs), being involved in cilia function and/or assembly . IFT-A polymerises interacts with IFT-B, and uses an array of β-propeller and TPR domains to create 'carriages' of the IFT train that engage TULP adaptor proteins . The β-propeller domains of IFT140 contact the β-propeller domains of IFT121 from the adjacent complex .
ELP1, three-helical bundle (HB_ELP1)
Type: Domain

This entry represents the helical bundle domain found within the C-terminal dimerisation domain of Elongator complex protein 1 (ELP1), from eukaryotes.

Elongator is a conserved protein complex implicated in multiple processes including regulation of transcription, alpha-tubulin acetylation and tRNA modification. Mutations in the ELP1 gene have been shown to cause the neurodegenerative disease familial dysautonomia . The C-terminal dimerisation domain consists of 28 α-helices organised in three domains: an elongated α-solenoid domain (helices 1 to 14); a TPR domain, formed by six double-helix repeats (helices 15 to 26); and a three-helix bundle, C-terminal cap (helices 26 to 28) . ELP1 self-association contributes to its stability and is important for Elongator assembly . ELP1 is considered to function both as a scaffold, for Elongator complex ELP2 and ELP3 binding, and as a docking site for various factors that regulate Elongator activity . Also known as IKAP, ELP1 acts as a regulator of IkB kinase complex involved in proinflammatory cytokine signalling .
IFT121-like, zinc finger domain (Znf_IFT121-like)
Type: Domain

This entry represents the zinc finger rubredoxin-like fold domain at the C-terminal of IFT121.

This domain is also found in the IFT121 homologue WDR19 (also known as IFT144) proteins which are similarly components of the IFT complex A and are involved in involved in ciliogenesis and ciliary protein trafficking . These proteins contain two tandem zinc finger domains ; this entry represents the second one.

IFT121 (also known as WDR35) is a component of the IFT complex A (IFT-A), which is required for retrograde ciliary transport and entry into cilia of G protein-coupled receptors that is involved in ciliogenesis and ciliary protein trafficking . This protein plays a role in cilia assembly and maintenance . IFT121 contains a zinc finger with rubredoxin-like fold . Knock-out IFT121 cells showed defective retrograde trafficking within cilia .
DNA polymerase II large subunit DP2, central domain (PolC_DP2_central_dom)
Type: Domain

This entry represents the central domain of DNA polymerase II large subunit from Pyrococcus abyssi (PolC) and similar sequences mainly found in archaea. This domain, which is found adjacent

, shows an α-β configuration .
DNA polymerase II large subunit DP2, catalytic domain (PolC_DP2_cat_dom)
Type: Domain

This entry represents the catalytic domain of DNA polymerase II large subunit from Pyrococcus abyssi (PolC) and similar sequences mainly found in archaea. This domain is found between

and

; it shows a six-stranded double-psi β-barrel (DPBB) .
Sec20, C-terminal (Sec20_C)
Type: Domain

Sec20 is a membrane glycoprotein and a SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) involved in retrograde transport from the Golgi to the endoplasmic reticulum (ER) . It is also required for N- and O-glycosylation in the Golgi .

This entry represents the C-terminal region of Sec20 and related proteins such as transport protein BOS1 and AtNPSN11.
SpoVR protein-like, N-terminal (SpoVR_N)
Type: Domain

This entry represents a domain found at the N-terminal of the stage V sporulation protein R, YcgB from E.coli and related proteins. Stage V sporulation protein R is involved in spore cortex formation . Little is known about cortex biosynthesis, except that it depends on several sigma E controlled genes, including spoVR . YcgB has been suggested to be part of a conserved signalling pathway with YeaH and YeaG. This pathway may be involved in nitrogen metabolism (see Supplementary note 5 in ).
Anti-CBASS protein Acb1-like, C-terminal domain (Acb1-like_C)
Type: Domain

This domain is found at the N terminus end of Anti-CBASS protein Acb1 from Sphingomonas paeninsulae , covering the whole length of the protein in Bacteriophage T4 and in related sequences from tailed bacteriophages and proteobacterial prophages. Abc1 counteracts or regulates the endogenous CBASS (cyclic oligonucleotide-based antiphage signalling system) antiviral defence system. It is a phosphodiesterase that enables metal-independent hydrolysis of the host cyclic di- and trinucleotide CBASS signals such as 3'3'-cGAMP, 3'3'cUA, and 3'3'3'-cAAA .
COPA/B, TPR domain (TPR_COPA_B)
Type: Domain

This entry represents the TPR domain found in Coatomer subunits alpha and beta (COPA1-3, COPB2 and COB21-3), from eukaryotes. The domain adopts an α-solenoid fold. Coatomer complexes function in the sorting and trafficking of proteins between subcellular organelles . Coat protein I (COPI)-coated vesicles mediate retrograde transport from the Golgi to the endoplasmic reticulum (ER), as well as transport within the Golgi . The Coatomer protein complex subunit beta 2 (COPB2) is involved in the formation of the COPI coatomer protein complex. COPB2 is a vital oncogene in many cancer types that regulates multiple biological behaviours of tumour cells, including proliferation, survival, tumourigenesis, invasion, and metastasis . COPA constitutes part of COPI, playing a role in the retrograde transport of cargo proteins between the Golgi and the ER and the movement of vesicles within the Golgi .
Corticotropin-releasing factor binding protein, N-terminal domain (CRF-BP_N)
Type: Domain

This entry corresponds to the N-terminal domain from eukaryotic corticotropin-releasing factor binding proteins (CRF-BP or CRH-BP).

Corticotropin-releasing hormone (CRH) plays multiple roles in vertebrate species. In mammals, it is the major hypothalamic releasing factor for pituitary adrenocorticotropin secretion, and is a neurotransmitter or neuromodulator at other sites in the central nervous system. In non-mammalian vertebrates, CRH not only acts as a neurotransmitter and hypophysiotropin, it also acts as a potent thyrotropin-releasing factor, allowing CRH to regulate both the adrenal and thyroid axes, especially in development. CRH-BP is thought to play an inhibitory role in which it binds CRH and other CRH-like ligands and prevents the activation of CRH receptors. There is however evidence that CRH-BP may also exhibit diverse extra and intracellular roles in a cell specific fashion and at specific times in development .
Corticotropin-releasing factor binding protein, C-terminal domain (CRF-BP_C)
Type: Domain

This entry corresponds to the C-terminal domain of the eukaryotic corticotropin-releasing factor binding proteins (CRF-BP or CRH-BP).

Corticotropin-releasing hormone (CRH) plays multiple roles in vertebrate species. In mammals, it is the major hypothalamic releasing factor for pituitary adrenocorticotropin secretion, and is a neurotransmitter or neuromodulator at other sites in the central nervous system. In non-mammalian vertebrates, CRH not only acts as a neurotransmitter and hypophysiotropin, it also acts as a potent thyrotropin-releasing factor, allowing CRH to regulate both the adrenal and thyroid axes, especially in development. CRH-BP is thought to play an inhibitory role in which it binds CRH and other CRH-like ligands and prevents the activation of CRH receptors. There is however evidence that CRH-BP may also exhibit diverse extra and intracellular roles in a cell specific fashion and at specific times in development .