SII-SWORD/CoKE huggingface dataset:
Histidine acid phosphatase active site (Acid_Pase_AS)
Type: Active_site

Histidine acid phosphatases are a heterogeneous group of proteins that hydrolyse phosphate esters, optimally at low pH. It has been shown that a number of acid phosphatases, from both prokaryotes and eukaryotes, share two regions of sequence similarity, each centred around a conserved histidine residue. These two histidines seem to be involved in the enzymes' catalytic mechanism . The first histidine is located in the N-terminal section and forms a phosphohistidine intermediate while the second is located in the C-terminal section and possibly acts as proton donor.
Ubiquitin-specific peptidase 24, UBA domain (USP24_UBA)
Type: Domain

Ubiquitin-specific peptidase 24 (USP24, MEROPS identifier C19.047) is a de-ubiquitinating enzyme that is associated with late-onset Parkinson's Disease . The enzyme is known to remove ubiquitin from damage-specific DNA-binding protein 2 (DDB2), increasing its stability. DDB2 is involved in DNA damage recognition in the nucleotide excision repair pathway, and is a component of an E3 ligase that targets XPC, histones and DDB2 itself . USP24 also de-ubiquitinates p53, and cells are resistant to apoptosis following UV irradiation if USP24 is depleted because p53 is stabilized . Single-nucleotide polymorphisms of the USP24 gene have been identified in lung cancer malignancy and could be diagnostic markers for the disease . The USP24 gene is up-regulated when the USP9X gene is down-regulated by shRNA, leading to increased survival of B-cell myeloma cells . USP24 positively regulates ferritinophagy, a process in which ferritin is degraded in lysosomes and releases free iron .

This entry represents the N-terminal ubiquitin-associated (UBA) domain of UBP24.
SWI/SNF-like complex subunit BAF250, C-terminal (BAF250_C)
Type: Domain

This domain can be found in the mammalian BAF250a/b and its homologue osa from fruit flies . They are part of the SWI/SNF-like ATP-dependent chromatin remodelling complex that regulates gene expression through regulating nucleosome remodelling. In humans there are two BAF250 isoforms, BAF250a/ARID1a and BAF250b/ARID1b. BAF250a/b may be E3 ubiquitin ligases that target histone H2B .
AUX/IAA domain (AUX/IAA_dom)
Type: Domain

Transcription of the AUX/IAA family of genes is rapidly induced by the plant hormone auxin . Some members of this family are longer and contain an N-terminal DNA binding domain, such as

. This entry represents the C-terminal region of the AUX/IAA proteins. The function of this region is uncertain.
3'-5' exoribonuclease Rv2179c-like domain (Rv2179c-like)
Type: Domain

This entry represents a domain found in a group of divergent 3' exoribonucleases. The proteins constitute a typical RNase fold, where the active site residues form a magnesium catalytic centre. The protein of the solved structure readily cleaves 3' overhangs in a time-dependent manner. It is similar to DEDD-type RNases and is an unusual ATP-binding protein that binds ATP and dATP. It forms a dimer in solution and both protomers in the asymmetric unit bind a magnesium ion through Asp-6 .

Proteins containing this domain also include 3'-5' exonuclease dexA from bacteriophage T4. It may play a role in the final step of host DNA degradation, by scavenging DNA into mononucleotides .
Fructose-1-6-bisphosphatase class I, N-terminal (FBPase_N)
Type: Domain

Fructose-1,6-bisphosphatase (FBPase) is a critical regulatory enzyme in gluconeogenesis that catalyses the removal of 1-phosphate from fructose 1,6-bis-phosphate to form fructose 6-phosphate . Five different classes (or types) of FBPases have been identified based on their amino acid sequences, with class I most widely distributed among living organisms .

This entry represents the N terminus of the FBPase class 1 family.
Sox 7/17/18, central domain (Sox7/17/18_central)
Type: Domain

This is the central region of eukaryotic SOX17 and 18 transcription factor proteins . It lies just downstream of the HMG-box domain, and is followed by a C-terminal domain.
Nuclear receptor-binding factor 2, MIT domain (NRBF2_MIT)
Type: Domain

This domain is the MIT (microtubule interaction and trafficking) domain of nuclear receptor-binding factor 2 (NRBF2) in higher eukaryotes. It is a coiled-coil region. NRBF2 plays an essential role in autophagy, the cellular pathway that degrades long-lived proteins and other cytoplasmic contents through lysosomes. NRBF2 binds Atg14L - a Beclin-binding protein - directly via the MIT domain and enhances Atg14L-linked Vps34 kinase (a class III phosphatidylinositol-3 kinase) activity and autophagy induction .
Svf1-like, C-terminal (Svf1-like_C)
Type: Domain

This entry represents the C-terminal lipocalin-like domain of stress survival proteins such as survival factor 1 (Svf1). The protein Svf1 is required for yeast survival under conditions of oxidative stress, including cold stress . Cells deficient in Svf1 have increased levels of reactive oxygen species (ROS) under certain conditions. Svf1 affects cellular survival in part via modulation of the sphingolipid metabolic pathway . Two Svf1 family proteins have been identified in the genome of Schizosaccharomyces pombe (Svf1 and Svf2).

Svf1 is a ceramide binding protein that contributes to sphingolipid metabolism at Golgi compartments and its membrane-targeting is important to maintain flux of ceramides into complex sphingolipids. Svf1 consists of two lipocalin-like domains and binds ceramide via a hydrophobic pocket that is located at the interface between these two domains . Two histidine residues located in a small predicted α-helical cap covering the hydrophobic pocket, are essential for the ceramide binding. Their mutation results in loss of ceramide binding as well as cis-Golgi targeting of the protein. The arrangement of two tandem lipocalin-like domains is reminiscent to AttH-like proteins (

).
Domain of unknown function DUF5106 (DUF5106)
Type: Domain

This domain, found in Bacteroidetes proteins, is frequently associated with a putative thioredoxin-like domain (

). The function of this domain is not known.
Domain of unknown function DUF5107 (DUF5107)
Type: Domain

This domain is found in a range of different bacterial species. In many proteins it lies N-terminal to a TPR-repeat region at the C terminus, including the uncharacterised protein YphG from Escherichia coli.
Metallo-carboxypeptidase, C-terminal domain (Metallo_peptidase_C)
Type: Domain

This domain represents the C-terminal immunoglobulin-like domain of metallo-carboxypeptidase Csd4, an helical cell shape-determining peptidoglycan hydrolase. The structural elements of this domain form a Ca2+ binding-channel, the Ca2+ being co-ordinated by six ligand-atoms .
Carboxypeptidase M99, beta-barrel domain (Beta-barrel_M99)
Type: Domain

This is the central, β-barrel domain of the metallo-carboxypeptidase that maintains helical cell-shape in Helicobacter. It shows a novel fold. It has a highly positively charged surface which contributes to a high overall isoelectric point. A calcium-binding channel is formed from residues in the C-terminal Ig-like domain in conjunction with some of the long side-chains of residues from strands β14 and β18 of this domain .
Putative outer membrane lipoprotein-sorting protein (Put_LolA-like)
Type: Family

This is likely to be a family of outer-membrane lipoprotein-sorting proteins.
Domain of unknown function DUF5108 (DUF5108)
Type: Domain

The domain is found C-terminal to a Fasciclin domain (

). It is found in Bacteroidetes proteins.
Domain of unknown function DUF5110 (DUF5110)
Type: Domain

This domain is found C-terminal in some glycoside hydrolase family 31 proteins (

). It adopts a β-sandwich fold and could be responsible for the stabilisation of the catalytic domain rather than for substrate binding, given that no interactions between this domain and the active-site pocket are observed in the proteins that are currently structurally characterised . In glucosidase II, this domain is involved in a network of interactions with the regulatory beta-subunit .
Domain of unknown function DUF5111 (DUF5111)
Type: Domain

This domain is found in SusE, a putative starch-processing family (

). It is possible that this domain represents a substrate-binding site.
Domain of unknown function DUF5112 (DUF5112)
Type: Domain

This function of this domain is not known.
Domain of unknown function DUF5113 (DUF5113)
Type: Domain

This domain is frequently found downstream of

in duplicate.
Domain of unknown function DUF5114 (DUF5114)
Type: Domain

This family lies further downstream of DUF5111 (

) on proteins from Bacteroidetes of the SusE family (

).
Outer membrane protein SusF, N-terminal domain (SusF_N)
Type: Domain

This entry represents a domain found N-terminal in outer membrane protein SusF from Bacteroides thetaiotaomicron and similar sequences from bacteroidetes. SusF is a starch-binding protein organised into three tandem domains packed against each other: N-terminal (this entry), middle, and C-terminal. The latter two (

) are common to SusE and SusF.

This domain forms a β-barrel that is similar in overall-fold and topology to several immunoglobulin superfamily domains found in cell adhesion proteins .
Protein of unknown function DUF5119 (DUF5119)
Type: Family

This is a family of uncharacterised Bacteroidia sequences. It has been suggested that the Fim4B protein from Bacterioides ovatus represents the base protein (or anchoring subunit) of the pilus (fimbrius) complex that protrudes from the bacterial surface .
Ribonuclease, PIN domain (Ribonuclease_PIN)
Type: Domain

This is a PIN domain found in eukaryotic ribonuclease Nob1 and archaeal ribonuclease VapC1 .

RNA-binding protein NOB1 has a nuclear location and contains a PIN domain and binds a single zinc ion. Budding yeast Nob1 is involved in proteasomal and 40S ribosomal subunit biogenesis . It is also required for maturation of the small subunit ribosomal RNA by catalyzing cleavage at site D after export of the preribosomal subunit into the cytoplasm. Nob1 is also found in archaea, where it is manganese-dependent and also processes RNA-substrates . This domain can also be found in VapC1, which is a toxic component and a ribonuclease of a toxin-antitoxin (TA) module .

PIN domains are small protein domains identified by the presence of three strictly conserved acidic residues. Apart from these three residues, there is poor sequence conservation . PIN domains are found in eukaryotes, eubacteria and archaea. In eukaryotes they are ribonucleases involved in nonsense mediated mRNA decay and in processing of 18S ribosomal RNA . In prokaryotes, they are the toxic components of toxin-antitoxin (TA) systems, their toxicity arising by virtue of their ribonuclease activity. The PIN domain TA systems are now called VapBC TAs(virulence associated proteins), where VapB is the inhibitor and VapC, the PIN-domain ribonuclease toxin .
Pyruvate:ferredoxin oxidoreductase, core domain II (PFOR_II)
Type: Domain

This is a core domain of the anaerobic enzyme pyruvate:ferredoxin oxidoreductase and is necessary for inter subunit contacts in conjunction with domains I and IV .
Domain of unknown function DUF5117 (DUF5117)
Type: Domain

This domain may fall upstream of a met-zincin domain.
Periplasmic sensor domain (Sensor_dom)
Type: Domain

This is a conserved periplasmic sensor domain found in histidine kinases, diguanylate cyclases/phosphodiesterases and methyl-accepting chemotaxis proteins . In Pseudomonas aeruginosa, this is the sensor domain in the c-di-GMP phosphodiesterase BifA that regulates biofilm formation and in sensor kinase AruS that regulates arginine degradation pathways . These results suggest that this domain might bind arginine or a related compound.
C-terminal domain of two-partite extracellular sensor domain (CHASE6_C)
Type: Domain

CHASE6 was originally described as a two-partite extracellular (periplasmic) sensor domain found in histidine kinases and HD-GYP-type c-di-GMP-specific phosphodiesterases and assigned to COG4250 in the COG database. Subsequently, its N-terminal part has been described as a separate DICT (DIguanylate Cyclases and Two-component systems) domain (

) (Aravind L., Iyer LM, Anantharaman V. (2010) Natural history of sensor domains in the bacterial signalling systems. In: Sensory Mechanisms in Bacteria: Molecular Aspects of Signal Recognition ((Spiro S, Dixon R, eds), pp. 1-38. Caister Academic Press, Norfolk, UK). The current entry contains only the C-terminal part of the original CHASE6 domain described in , which is found primarily in cyanobacteria.
Periplasmic sensor domain CHASE7 (CHASE7)
Type: Domain

CHASE7 is a conserved periplasmic sensor domain found in histidine kinases and diguanylate cyclases/phosphodiesterases, including the diguanylate cyclase DgcQ (YedQ) that regulates biofilm formation and motility in Escherichia coli .
Periplasmic sensor domain CHASE8 (CHASE8)
Type: Domain

CHASE8 is a conserved periplasmic sensor domain found in histidine kinases, diguanylate cyclases/phosphodiesterases and methyl-accepting chemotaxis proteins, including the diguanylate cyclase DgcN (YfiN) that regulates biofilm formation and motility in Escherichia coli . In Pseudomonas aeruginosa, CHASE8 is the sensor domain in the diguanylate cyclase TpbB that regulates biofilm formation by controlling the levels of extracellular DNA .
Periplasmic sensor domain, extracellular (CHASE9)
Type: Domain

CHASE9 is a conserved extracellular (periplasmic) sensor domain found in histidine kinases, diguanylate cyclases/phosphodiesterases, methyl-accepting chemotaxis proteins, adenylate cyclases and protein serine phosphatases, including the c-di-GMP phosphodiesterases PdeI (YliE) of Escherichia coli .
Gammaproteobacterial periplasmic sensor domain GAPES3 (GAPES3)
Type: Domain

GAPES3 (GAmmaproteobacterial PEriplasmic Sensor) domain is a periplasmic sensor domain found in diguanylate cyclases/phosphodiesterases, including the c-di-GMP phosphodiesterases PdeK (YhjK) of Escherichia coli and HmsP of Yersinia pestis .
Gammaproteobacterial periplasmic sensor domain GAPES1 (GAPES1)
Type: Domain

GAPES1 (GAmmaproteobacterial PEriplasmic Sensor) domain is a periplasmic sensor domain found in diguanylate cyclases and methyl-accepting chemotaxis proteins, including the diguanylate cyclase DgcJ (YeaJ) that regulates biofilm formation and motility in Escherichia coli .
Rit1, DUSP-like domain (Rit1_DUSP-like)
Type: Domain

Rit1 modifies exclusively the initiator tRNA in position 64 using 5'-phosphoribosyl-1'-pyrophosphate as the modification donor. As the initiator tRNA participates both in the initiation and elongation of translation, the 2'-O-ribosyl phosphate modification discriminates the initiator tRNAs from the elongator tRNAs . This C-terminal domain shows similarity to dual specificity phosphatases (DUSPs) .
Gammaproteobacterial periplasmic sensor domain GAPES2 (GAPES2)
Type: Domain

GAPES2 (GAmmaproteobacterial PEriplasmic Sensor) domain is a periplasmic sensor domain found in diguanylate cyclases, including the diguanylate cyclase DgcI (YliF) of Escherichia coli . It contains three conserved Cys residues that might participate in thiol-disulfide exchange.
Gammaproteobacterial periplasmic sensor domain GAPES4 (GAPES4)
Type: Domain

GAPES4 (GAmmaproteobacterial PEriplasmic Sensor) domain is a periplasmic sensor domain found in various GGDEF- and EAL-containing proteins. In Escherichia coli, GAPES4 forms the N-terminal domain of the regulatory protein CsrD (YhdA) , which contains enzymatically inactive GGDEF and EAL domains and controls the degradation of two non-coding RNAs, CsrB and CsrC . In Vibrio cholerae, GAPES4-containing protein MshH (

) inhibits biofilm formation, apparently acting through the glucose-specific enzyme IIA .
Membrane-associated sensor domain (MASE4)
Type: Domain

MASE4 (Membrane-Associated SEnsor) is an integral membrane sensor domain found in various GGDEF domain proteins, including a functional diguanylate cyclase DgcT (YcdT) and the enzymatically inactive CdgI (YeaI) of Escherichia coli . In the Shiga toxin-producing enteroaggregative E. coli O104:H4, which caused the outbreak of the haemolytic uraemic syndrome in Germany in 2011, MASE4-containing diguanylate cyclase DgcX (

) was highly expressed, ensuring strong biofilm formation .
Membrane-associated sensor domain MASE3 (MASE3)
Type: Domain

MASE3 (Membrane-Associated SEnsor) is an integral membrane sensor domain of unknown specificity found in histidine kinases, diguanylate cyclases and protein phosphatases in various bacteria and archaea .
Domain of unknown function DUF5124 (DUF5124)
Type: Domain

DUF5124 is a domain of unknown function found in proteins from Bacteroidales.
Domain of unknown function DUF5123 (DUF5123)
Type: Domain

This function of this domain is not known. It is found in proteins from Bacteroidetes.
Domain of unknown function DUF5118 (DUF5118)
Type: Domain

This domain falls upstream of a met-zincin domain.
Domain of unknown function DUF5125 (DUF5125)
Type: Domain

This entry represents a domain of unknown function found in a group of proteins from Bacteroidetes. It is often found N-terminal to

.
Domain of unknown function DUF5121 (DUF5121)
Type: Domain

This domain has no known function.
Domain of unknown function DUF5126 (DUF5126)
Type: Domain

This domain lies C-terminal to DUF4959 (

).
Glycosyl hydrolase 94, catalytic domain (GH94_catalytic)
Type: Domain

This is the catalytic region of the superfamily of enzymes referred to as GH94, formerly known as glycosyltransferase family GT36 .

ChbP is a chitobiose phosphorylase that catalyses the reversible phosphorolysis of chitobiose into alpha-GlcNAc-1-phosphate and GlcNAc with inversion of the anomeric configuration. The full-length enzyme comprises a β sandwich domain and an (α/α)(6) barrel domain. The α-helical barrel component of the domain, represented in this entry, is the catalytic region .
Glutaminase A, N-terminal domain (GtaA_N)
Type: Domain

This domain is found towards the N terminus of Glutaminase A (GtaA), an enzyme from Aspergillus that catalyses the hydrolysis of glutamine to glutamic acid and plays a key role in nitrogen metabolism . It was previously known as DUF5127. Members of this group of proteins are mainly found in fungi and bacteria.
MucB/RseB, N-terminal (MucB/RseB_N)
Type: Domain

This entry represents the N-terminal domain of sigma-E factor regulatory protein RseB and sigma factor AlgU regulatory protein MucB. RseB negatively modulates the activity of sigma-E (RpoE) by stabilizing RseA under non-stress conditions . MucB is a negative regulator of the sigma factor AlgU. It plays a role in the differentiation of P.aeruginosa into the alginate-producing form .
Domain of unknown function DUF5129 (DUF5129)
Type: Domain

DUF5129 is domain of unknown function found in uncharacterised proteins from Actinobacteria.
MucB/RseB, C-terminal (MucB/RseB_C)
Type: Domain

This entry represents the C-terminal domain of sigma-E factor regulatory protein RseB and sigma factor AlgU regulatory protein MucB. MucB plays a role in the differentiation of P. aeruginosa into the alginate-producing form . RseB negatively modulates the activity of sigma-E (RpoE) by stabilizing RseA under non-stress conditions . The small C-terminal domain of RseB is responsible for interaction with RseA .
Protein of unknown function DUF5130 (DUF5130)
Type: Family

This entry represents a family of uncharacterised proteins from Actinobacteria, including MSMEG_4692/MSMEI_4575 from Mycolicibacterium smegmatis (

), part of a respiratory supercomplex .
Modulator of levamisole receptor-1 (MOLO1)
Type: Family

MOLO1 is a one-pass transmembrane protein that contains a single extracellular globular domain. It is a positive regulator of levamisole-sensitive acetylcholine receptors in Caenorhabditis elegans (

) . These receptors are Cys-loop ligand-gated ion channels, and MOLO1 is an auxiliary subunit of the gated channel. The proteins carry a Rossmann fold.
Chromosome partition protein MukF, winged-helix domain (MukF_WHTH)
Type: Domain

This entry represents the N-terminal winged helix-turn-helix domain of MukF . MukF is involved in chromosome condensation, segregation and cell cycle progression. MukE along with MukF interact with MukB in vivo forming a complex, which is required for chromosome condensation and segregation in Escherichia coli . The Muk complex appears to be similar to the SMC-ScpA-ScpB complex in other prokaryotes where MukB is the homologue of SMC .
Chromosome partition protein MukF, middle domain (MukF_M)
Type: Domain

This entry represents the middle coiled-coil domain of MukF . MukF is involved in chromosome condensation, segregation and cell cycle progression. MukE along with MukF interact with MukB in vivo forming a complex, which is required for chromosome condensation and segregation in Escherichia coli . The Muk complex appears to be similar to the SMC-ScpA-ScpB complex in other prokaryotes where MukB is the homologue of SMC .
Chromosome partition protein MukF, C-terminal domain (MukF_C)
Type: Domain

This entry represents the C-terminal domain of MukF. MukF is involved in chromosome condensation, segregation and cell cycle progression. MukE along with MukF interact with MukB in vivo forming a complex, which is required for chromosome condensation and segregation in Escherichia coli . The Muk complex appears to be similar to the SMC-ScpA-ScpB complex in other prokaryotes where MukB is the homologue of SMC . The C-terminal domain of MukF is thought to bind to MukE and MukB .
tRNA(Met) cytidine acetyltransferase TmcA, tRNA-binding domain (TmcA_tRNA_bind)
Type: Domain

This domain, found at the C-terminal of tRNA(Met) cytidine acyltransferase, may be involved in tRNA-binding .
PROP1-like, PPR domain (PROP1-like_PPR_dom)
Type: Domain

This entry represents the PPR domain of Proteinaceous RNase P 1, chloroplastic/mitochondrial from Arabidopsis thaliana (PRORP1) and similar eukaryotic sequences. PRORPs are a class of RNA processing enzymes that catalyse maturation of the 5' end of precursor tRNAs in eukaryotes . This domain consists of up to eleven α-helices. The region serves to enhance the activity of the metallonuclease domain .
Membrane-associated sensor MASE5 (MASE5)
Type: Domain

MASE5 is an integral membrane sensor domain found in various GGDEF domain proteins, including a diguanylate cyclase DgcY (EcSMS35_1716) from multidrug-resistant environmental isolate Escherichia coli SMS-3-5 .
Zinc finger domain-containing protein 24, 3CxxC-type zinc finger (ZCCHC24_Znf-3CxxC)
Type: Domain

This entry represents the Znf-3CxxC domain in ZCCHC24.

Zinc finger domain-containing protein 24 (ZCCHC24) encodes a protein containing two zinc finger domains from the Znf-CCHC and Znf-3CxxC superfamilies . This protein contains a 3CxxC-type zinc finger (

) next to the C-terminal domain (

), these subdomains are represented by

.
OSK domain (OSK)
Type: Domain

This entry represents the OSK domain defined by Jeske and colleagues . The domain is related to SGNH hydrolases but lacks the active site residues. The domain binds to RNA . Proteins containing this domain include maternal effect protein oskar, which is required to keep nos RNA and staufen protein at the posterior pole in Drosophila melanogaster .
Rit1, N-terminal domain (Rit1_N)
Type: Domain

This entry represents the N-terminal domain of the enzyme Rit1 (tRNA A64-2'-O-ribosylphosphate transferase) which modifies exclusively the initiator tRNA in position 64 using 5'-phosphoribosyl-1'-pyrophosphate as the modification donor. As the initiator tRNA participates both in the initiation and elongation of translation, the 2'-O-ribosyl phosphate modification discriminates the initiator tRNAs from the elongator tRNAs . The N-terminal domain is the most conserved region of the protein .