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Search results 1 to 100 out of 1733 for Was

Category restricted to ProteinDomain (x)

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Categories

Category: ProteinDomain
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Type Details Score
Protein Domain
IPR027641 | WASP
Type: Family
Description: This entry represents the Actin nucleation-promoting factor WAS (WASP). The WASP proteins signal to the cytoskeleton through the Arp2/3 complex, an actin-nucleating assembly that regulates the structure and dynamics of actin filament networks at the leading edge of the cell []. The activity of WASP can be regulated by the Rho-family GTPase, Cdc42 []. Mutations in WASP lead to the Wiskott-Aldrich syndrome, a paediatric disorder characterised by actin cytoskeletal defects in haematopoietic cells, leading clinically to thrombocytopenia, eczema and immunodeficiency [].Similar to mammalian WASP proteins, Wsp1 and Las17 also has a role in regulating actin assembly [, ]. In Saccharomyces cerevisiae, Las17 is the primary activator of Arp2/3-driven actin nucleation and is required for membrane invagination during endocytosis []. Las17 can also nucleate actin filaments independently of Arp2/3 through its polyproline domain [].WASP family members have unique N-terminal regions, followed by a central segment rich in proline, and a common C-terminal region. Their conserved C-terminal VCA domain consists of two WH2 (WASP homology 2) domains ("V"referring to either a single or multiple WH2 domains), followed by a connector domain ("C") and an acidic short extension ("A"). In the VCA region, the WH2 domain(s) bind G-actin, whereas the CA domain binds Arp2/3 complex []. Their distinct N-terminal region enables family members to activate Arp2/3 in response to differentupstream signals.
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Protein Domain
IPR025343 | DUF4099
Type: Family
Description: This family of uncharacterised proteins was found by clustering human gut metagenomic sequences [].
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Protein Domain
IPR031370 | Aim3
Type: Family
Description: Altered inheritance of mitochondria protein 3 (Aim3) was first identified as an actin patch protein []. Later, it was found to inhibit barbed-end actin filament elongation []. It may be involved in mitochondrion organisation and biogenesis [].
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Protein Domain
IPR018633 | DUF2357
Type: Domain
Description: This entry was previously the N-terminal portion of DUF524 () before it was split into two. This domain has no known function. It is predicted to adopt an all beta secondary structure pattern followed by mainly α-helical structures [].
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Protein Domain
IPR038848 | CABYR
Type: Family
Description: CABYR was originally isolated from spermatoza and was thought to be testis specific, but has been observed in lung and brain tumours []. It is a polymorphic calcium binding protein that is phosphorylated during capacitation [].
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Protein Domain
IPR030053 | TAS2R7
Type: Family
Description: T2Rs (taste receptor type 2) function as bitter taste receptors []. The activation of the human bitter taste receptors, TAS2Rs, by polyphenol compounds was analysed. TAS2R7 was the only receptor stimulated by the anthocyanin malvidin-3-glucoside [].
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Protein Domain
IPR029725 | WFDC9
Type: Family
Description: Protein WFDC9 was isolated in a region containing several WAP proteins and was defined as a WAP protein; however, it doesn't contain a classical WAP domain. Its function is not clear.
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Protein Domain
IPR025051 | DUF3990
Type: Family
Description: This entry represents a family of uncharacterised proteins that was originally found by clustering human gut metagenomic sequences [].
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Protein Domain
IPR025048 | DUF3987
Type: Family
Description: This entry represents a family of uncharacterised proteins that was originally found by clustering human gut metagenomic sequences [].
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Protein Domain
IPR045372 | YidB
Type: Family
Description: This entry includes the uncharacterised protein YidB from E. coli. This entry was previously a subset of the DUF937 family.
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Protein Domain
IPR033557 | LEXM
Type: Family
Description: Lexm/Lem was reported to be involved on T-cell metabolism, but the validity of these findings is controversial [].
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Protein Domain
IPR022820 | UPF0758_YicR
Type: Family
Description: UPF0758 was previously known as the radC family. The name was assigned according to the radC102 mutant of E. coli which was later demonstrated to be an allele of the transcription-repair-coupling factor recG [, ]. It has been described as a putative JAMM-family deubiquitinating enzyme, but its function remains to be determined [].This entry represents the YicR subfamily, found in the Enterobacteriaceae.
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Protein Domain
IPR020891 | UPF0758_CS
Type: Conserved_site
Description: UPF0758 was previously known as the radC family. The name was assigned according to the radC102 mutant of E. coli which was later demonstrated to be an allele of the transcription-repair-coupling factor recG [, ]. It has been described as a putative JAMM-family deubiquitinating enzyme, but its function remains to be determined [].
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Protein Domain
IPR002918 | Lipase_EstA/Esterase_EstB
Type: Family
Description: This family represents lipase estA and extracellular esterase estB. Lipase estA (also known as lipase LipA) was initially identified in Bacillus subtilis as a lipase that was active toward p-nitrophenyl esters and triacylglycerides, displaying a marked preference for esters with C8 acyl groups []. A second, secreted lipase (LipB) was then identified in Pseudomonas fluorescens []. However, it is likely that this second enzyme functions as an esterase, rather than a lipase []. It has therefore been renamed extracellular esterase estB.
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Protein Domain
IPR009346 | GRIM-19
Type: Family
Description: This family consists of several eukaryotic gene associated with retinoic-interferon-induced mortality 19 (GRIM-19) proteins. GRIM-19, was reported to encode a small protein primarily distributed in the nucleus and was able to promote cell death induced by IFN-beta and RA. A bovine homologue of GRIM-19 was co-purified with mitochondrial NADH:ubiquinone oxidoreductase (complex I) in bovine heart. Therefore, its exact cellular localisation and function are unclear. It has now been discovered that GRIM-19 is a specific interacting protein which negatively regulates Stat3 activity [].
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Protein Domain
IPR022598 | FcoT_ThioEstase
Type: Family
Description: Proteins in this family have a HotDog fold. This family was formerly known as DUF2662. The structure of FcoT from M. tuberculosis []suggested a thioesterase function. Assays showed that this protein was a thioesterase with a preference for long chain fatty acyl groups []. The maximal Kcat was observed for palmitoyl-CoA, although longer and shorter molecules were also cleaved. In solution this protein forms a homo-hexameric complex.
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Protein Domain
IPR031388 | Tda11
Type: Family
Description: Tda11 was identified as a protein affecting topoisomerase I-induced DNA damage from a high-throughput screening []. It is a potential Cdc28p substrate []. Its function is not clear.
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Protein Domain
IPR018700 | DUF2204
Type: Family
Description: This family of hypothetical prokaryotic proteins has no known function. However, this family was identified as belonging to the nucleotidyltransferase superfamily [, ].
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Protein Domain
IPR018891 | Abortive_phage_infection
Type: Family
Description: This family of proteins was identified as an abortive infection phage resistance protein often found in restriction modification system operons [].
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Protein Domain
IPR043876 | DUF5856
Type: Family
Description: This is a family of uncharacterised proteins of unknown function predominantly found in viruses. This family was also found in Bacteria.
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Protein Domain
IPR026475 | Archaetidylserine_synthase
Type: Family
Description: The activity CDP-2,3-di-O-geranylgeranyl-sn-glycerol:L-serine O-archaetidyltransferase (archaetidylserine synthase) was demonstrated experimentally in Methanothermobacter thermautotrophicus. Members represent an exception within the broader family of CDP-diacylglycerol-serine O-phosphatidyltransferases [].
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Protein Domain
IPR026102 | BCAP
Type: Family
Description: BCAP is a centriolar satellite protein and inhibitor of ciliogenesis. It was also known as ODF2-like protein due to its homology to ODF2, a centriolar appendage protein [].
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Protein Domain
IPR028685 | LPPR3
Type: Family
Description: Phospholipid phosphatase-related protein type 3, also known as plasticity-related gene 2 protein (PRG-2), was identified as a related gene to PRG-1 [], but has not been characterised yet.
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Protein Domain
IPR038955 | PriA_fungi
Type: Family
Description: PriA was identified in Lentinula edodes (Shiitake mushroom) as a gene that may play a role during the beginning of fruiting [, ].
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Protein Domain
IPR024385 | DUF3854
Type: Domain
Description: This domain of unknown function was found by clustering human gut metagenomic sequences []. It may be related to the Toprim domain.
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Protein Domain
IPR009267 | NTP_transf_6
Type: Family
Description: This family consists of several hypothetical bacterial proteins of unknown function. This family was recently identified as belonging to the nucleotidyltransferase superfamily [].
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Protein Domain
IPR005274 | IM_pro_YhjD
Type: Family
Description: This family, including YhjD in E. coli, is a conserved inner membrane protein []. Its homologue, YihY, was incorrectly assigned to be ribonuclease BN previously [].
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Protein Domain
IPR019710 | DUF4226
Type: Family
Description: This entry represents an uncharacterised family of proteins belonging to Mycobacteria. It was previously incorrectly annotated as biofilm regulator BssS (also known as YliH).
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Protein Domain
IPR025269 | SAM-like_dom
Type: Domain
Description: This domain was originally identified by clustering human gut metagenomic sequences []. It appears related to the N-terminal domain of phage integrases.
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Protein Domain
IPR027783 | Bacterial_PH-related
Type: Domain
Description: This domain is found in proteins with unknown function and appears to be related to bacterial Pleckstrin homology (PH) domain () []. It was formerly known as DUF2679.
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Protein Domain
IPR037645 | KCT2
Type: Family
Description: The function of KCT2 is not known. It was isolated from a library from human keratinocytes and is predicted to be a type I transmembrane protein [].
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Protein Domain
IPR037541 | MFS_YfcJ
Type: Family
Description: This is a family of uncharacterized MFS-type transporters. YfcJ is a sugar efflux transporter candidate. Deletion of yfcJ was found to increase intracellular arabinose concentrations [].
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Protein Domain
IPR035283 | Fmp23
Type: Family
Description: FMP23 gene encodes a putative mitochondrial protein involved in iron-copper homoeostasis. It was observed to be induced in response to ATX1 deletion and high copper conditions [, ].
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Protein Domain
IPR023162 | Apc36109-like_dom_sf
Type: Homologous_superfamily
Description: This domain superfamily was determined from the crystal structure of APC36109 from Bacillus stearothermophilus (Geobacillus stearothermophilus). It is found in a family of proteins of unknown function.
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Protein Domain
IPR039108 | CCDC120
Type: Family
Description: Coil-coiled domain-containing protein 120 (CCDC120) was first identified as a centrosome protein []. Later, it was found to interact with cytohesin-2 to regulate vesicular trafficking and neurite growth []. It is part of the centriole subdistal appendages (SDAs) that anchor microtubules in interphase cells [].
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Protein Domain
IPR004179 | Sec63-dom
Type: Domain
Description: This domain was named after the yeast Sec63 (or NPL1) (also known as the Brl domain) protein in which it was found. This protein is required for assembly of functional endoplasmic reticulum translocons [, ]. Other yeast proteins containing this domain include pre-mRNA splicing helicase BRR2, HFM1 protein and putative helicases.
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Protein Domain
IPR028278 | MRI
Type: Family
Description: CYREN is a cell-cycle-specific inhibitor of classical non-homologous end joining (cNHEJ) that promotes error-free repair by homologous recombination during the S and G2 phases (when sister chromatids are present) []. It was originally known as MRI (modulator of retrovirus infection), as it was isolated as a gene that could reverse the resistance to retroviral infection in a mutant cell line [].
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Protein Domain
IPR033746 | GGa_phosphorylase
Type: Family
Description: Glucosylglycerate phosphorylase (part of subfamily 18 of glycoside hydrolase family 13 (GH13_18) in CAZy) was previously thought to function as a sucrose phosphorylase, and was previously known as putative sucrose phosphorylase YcjM. However, studies have since shown it to be a glucosylglycerate phosphorylase, and to have no activity on sucrose [].
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Protein Domain
IPR026073 | GGNBP2
Type: Family
Description: Mouse gametogenetin binding protein 2 (GGNBP2) was found to interact with gametogenetin protein 1 (GGN1), which is the product of a testicular germ cell-specific gene specifically expressed from late pachytene spermatocytes through round spermatids. Therefore, GGNBP2 was suggested to be involved in spermatogenesis [].
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Protein Domain
IPR012105 | Sp17
Type: Family
Description: Sp17 was originally proposed to be a sperm-specific protein that plays a role in sperm-egg interactions by binding to the zona pellucida via two conserved heparin-binding motifs []. Later, it was found expressed in other tissues and may have a regulatory role in an A-kinase anchoring protein complex [, ].
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Protein Domain
IPR019266 | MRPS27
Type: Family
Description: MRPS27 was annotated initially as one of the mammalian small subunit ribosomal proteins although its function was not known []. The supernumerary mitochondrial ribosomal protein of the small subunit 27 (MRPS27) is a pentatricopeptide repeat domain (PPR) protein required for mitochondrial protein synthesis [].
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Protein Domain
IPR029383 | ARL6IP6
Type: Family
Description: ADP-ribosylation factor-like protein 6-interacting protein 6 (ARL6IP6) is a transmembrane helix present in the J2E erythro-leukaemic cell line, but not its myeloid variants. In tissues, ARL-6 mRNA was most abundant in brain and kidney. While ARL-6 protein was predominantly cytosolic, it is known to bind to SEC61-beta subunit of a protein conducting channel SEC61p [].
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Protein Domain
IPR029435 | TOPAZ1_dom
Type: Domain
Description: This domain is found in protein TOPAZ1, which may play an important role in germ cell development []. Homology suggests that it is a putative aspartate racemase.Protein TOPAZ1 was previously called testis and ovary-specific PAZ domain-containing protein 1 [], but the name was changed to Protein TOPAZ1 as it does not contain a PAZ domain.
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Protein Domain
IPR039239 | AJAP1
Type: Family
Description: Adherens junction-associated protein 1 (AJAP1, also known as shrew-1) was first discovered as a transmembrane protein of adherent junctions in epithelial cells. Later, it was found to act as a tumour suppressor in gliomas. It may affect cell motility, migration, invasion and proliferation [, ]. Homologues are found only in chordates.
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Protein Domain
IPR040461 | Hop2
Type: Family
Description: Homologous-pairing protein 2 (Hop2) is required for proper homologous pairing and efficient cross-over and intragenic recombination during meiosis [, , ].The mammalian HOP2 homologue, TBPIP, was first identified as a factor interacting with TBP-1, which binds to the human immunodeficiency virus, type 1 Tat protein []. Later, TBPIP was found to be an activator that specifically stimulates the homologous pairing catalyzed by DMC1 [].
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Protein Domain
IPR000839 | Porin_Oms28
Type: Family
Description: The outer membrane-spanning (Oms) proteins of Borrelia burgdorferi have been isolated and their porin activities characterised; 0.6-nS porin activity was found to reside in a 28kDa protein, designated Oms28 []. The gene sequence of oms28 was found to encode a 257-amino-acid precursor protein with a putative 24-amino-acid leader peptidase I signal sequence []. The Oms28 protein partly fractionated to the outer membrane, and was characterised by an average single-channel conductance of 1.1 nS in a planar lipid bilayer assay, confirming Oms28 to be a porin [].
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Protein Domain
IPR046778 | UPF0758_N
Type: Domain
Description: This domain is functionally uncharacterised, found at the N-terminal of the uncharacterised UPF0758 proteins from bacteria and archaea, and is approximately 90 amino acids in length. UPF0758 was previously known as the radC family, a name that was assigned according tothe radC102 mutant of E. coli which was later demonstrated to be an allele of the transcription-repair-coupling factor recG [, ]. UPF0758 has been described as a putative JAMM-family deubiquitinating enzyme, but its function remains to be determined []. Structure prediction using Colab notebook from AlphaFold DB suggests that it has an alpha bundle fold. It may contain two helix-hairpin-helix (HhH) motifs. This domain is found in association with [].
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Protein Domain
IPR031404 | Rrt14
Type: Family
Description: Rrt14 is a nucleolar protein whose function is not clear. It was identified in a screen for mutants with decreased levels of rDNA transcription []. It may be involved in ribosome biogenesis [].
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Protein Domain
IPR016072 | Skp1_comp_dimer
Type: Domain
Description: SKP1 (together with SKP2) was identified as an essential component of the cyclin A-CDK2 S phase kinase complex []. It was found to bind several F-box containing proteins (e.g., Cdc4, Skp2, cyclin F) and to be involved in the ubiquitin protein degradation pathway. A yeast homologue of SKP1 (P52286) was identified in the centromere bound kinetochore complex []and is also involved in the ubiquitin pathway []. In Dictyostelium discoideum (Slime mold) FP21 was shown to be glycosylated in the cytosol and has homology to SKP1 [].This entry represents a dimerisation domain found at the C-terminal of SKP1 proteins [], as well as in subunit D of the centromere DNA-binding protein complex Cbf3 []. This domain is multi-helical in structure, and consists of an interlocked herterodimer in F-box proteins.
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Protein Domain
IPR016073 | Skp1_comp_POZ
Type: Domain
Description: SKP1 (together with SKP2) was identified as an essential component of the cyclin A-CDK2 S phase kinase complex []. It was found to bind several F-box containing proteins (e.g., Cdc4, Skp2, cyclin F) and to be involved in the ubiquitin protein degradation pathway. A yeast homologue of SKP1 (P52286) was identified in the centromere bound kinetochore complex []and is also involved in the ubiquitin pathway []. In Dictyostelium discoideum (Slime mold) FP21 was shown to be glycosylated in the cytosol and has homology to SKP1 [].This entry represents a POZ domain with a core structure consisting of beta(2)/alpha(2)/beta(2)/alpha(2) in two layers, alpha/beta. This domain is found at the N-terminal of SKP1 proteins []as well as in subunit D of the centromere DNA-binding protein complex Cbf3 [].
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Protein Domain
IPR031716 | LCE6A
Type: Family
Description: LCE6A, late cornified envelope protein 6A, is found in mammals. It was identified in a large-scale screening experiment as being involved in the barrier function of the epidermis [].
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Protein Domain
IPR006908 | Herpes_UL49
Type: Family
Description: This is a family of herpesvirus UL49 tegument proteins. It was shown that interactions between herpesvirus envelope and tegument proteins may play a role in secondary envelopment during herpesvirus virion maturation.
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Protein Domain
IPR041527 | YhcG_N
Type: Domain
Description: This domain can be found at the N terminus of YhcG from E.coli. YhcG was identified in association with DNA processing enzymes, including the restriction complexes HsdMRS and McrABC, the integrases IntF and IntS, and the recombinase PinE [].
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Protein Domain
IPR026499 | S_glycosyl_SunS
Type: Family
Description: Members of this family include SunS, the S-glycosyltransferase that transfers a sugar (substrate is variable in reconstitution assays) onto the precursor of the glycopeptide sublancin, which once was thought to be a lantibiotic [].
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Protein Domain
IPR002771 | Multi_antbiot-R_MarC
Type: Family
Description: MarC is a protein that spans the plasma membrane multiple times and once was thought to be a multiple antibiotic resistance protein. The function for this family is unknown [].
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Protein Domain
IPR020920 | LldD
Type: Family
Description: This entry represents the bacterial L-lactate dehydrogenase, a member of the FMN-dependent alpha-hydroxy acid dehydrogenase family. It catalyses the oxidation of L-lactate to pyruvate [, ]. The lld operon was previously named lct [].
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Protein Domain
IPR036296 | SKP1-like_dim_sf
Type: Homologous_superfamily
Description: SKP1 (together with SKP2) was identified as an essential component of the cyclin A-CDK2 S phase kinase complex []. It was found to bind several F-box containing proteins (e.g., Cdc4, Skp2, cyclin F) and to be involved in the ubiquitin protein degradation pathway. A yeast homologue of SKP1 (P52286) was identified in the centromere bound kinetochore complex []and is also involved in the ubiquitin pathway []. In Dictyostelium discoideum (Slime mold) FP21 was shown to be glycosylated in the cytosol and has homology to SKP1 [].This entry represents the superfamily of a dimerisation domain found at the C-terminal of SKP1 proteins [], as well as in subunit D of the centromere DNA-binding protein complex Cbf3 []. This domain is multi-helical in structure, and consists of an interlocked herterodimer in F-box proteins.
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Protein Domain
IPR009364 | YdaT_toxin
Type: Domain
Description: YdaT toxin was first thought to be neutralised by the putative antitoxin YdaS () []but recent studies showed that both YdaS and YdaT can act independently as toxins and are regulated by RacR [].
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Protein Domain
IPR012917 | DUF3294
Type: Family
Description: This family was annotated as mitochondrial ribosomal protein Mrp8, based on the presumed similarity of the S.cerevisiae protein to an E.coli mitochondrial ribosomal protein. However, this similarity is spurious, and the function is not known.
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Protein Domain
IPR034443 | PB1A10.08
Type: Family
Description: The function of PB1A10.08 is not known. In a fission yeast study, it was identified as belonging to a group of late genes that are induced after meiotic divisions and whose expression remains high until the completion of sporulation [].
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Protein Domain
IPR022485 | SHCHC_synthase_MenH
Type: Family
Description: This protein catalyzes the formation of SHCHC, or (1 R,6 R)-2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate, by elmination of pyruvate from 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate (SEPHCHC) []. Note that SHCHC synthase activity previously was attributed to MenD, which in fact is SEPHCHC synthase.
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Protein Domain
IPR020310 | WFDC11
Type: Family
Description: Protein WFDC11 was isolated in a region containing several WAP proteins and were defined as WAP proteins, however, it does not contain a classical WAP domain. In rats, WFDC11 is expressed in the epididymis of the male reproductive tract [].
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Protein Domain
IPR007341 | Transgly_assoc
Type: Family
Description: This bacterial protein is predicted to be an integral membrane protein. Some family members have been annotated as transglycosylase-associated proteins, but no experimental evidence is provided. This family was annotated based on the information in .
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Protein Domain
IPR010867 | NPR_nonapeptide
Type: Repeat
Description: This is a nine residue repeat, which was called NPR after NonaPeptide Repeat. It is found in two malarial proteins and has the consensus EEhhEEhhP where h stands for a hydrophobic amino acid.
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Protein Domain
IPR034861 | RBM26
Type: Family
Description: RBM26, also known as cutaneous T-cell lymphoma (CTCL) tumor antigen se70-2, was identified as a cutaneous lymphoma (CL)-associated antigen []. It contains two RNA recognition motifs (RRMs). The RRMs may play some functional roles in RNA-binding or protein-protein interactions.
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Protein Domain
IPR007625 | Herpes_UL51
Type: Family
Description: UL51 protein is a virion protein. In Suid herpesvirus 1 (Pseudorabies virus), UL51 () was identified as a component of the capsid []. In Human herpesvirus 1 (HHV-1) there is evidence for post-translational modification of UL51 [].
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Protein Domain
IPR030425 | MS4A_4A
Type: Family
Description: Human membrane-spanning 4-domains subfamily A member 4A (MS4A4A) was identified as a member of the MS4A gene family []. Common variants of MS4A4A are associated with Alzheimer's disease [, ].
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Protein Domain
IPR029270 | LIX1
Type: Family
Description: This entry represents the limb expression 1 (LIX1) family. LIX1 was identified in a screen for genes transiently expressed during early chicken limb development []. It has homologues in human, mouse and Drosophila.
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Protein Domain
IPR023742 | FeS-repair_YftE
Type: Family
Description: YtfE was is also known as regulator of cell morphogenesis and NO signaling because it is involved in anaerobic NO protection []. It is part of a family of di-iron proteins involved in the repair of iron-sulphur clusters [, ].
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Protein Domain
IPR005773 | YopR
Type: Family
Description: This model identifies the generic virulence translocation proteins in bacteria. It derives its name:'Yop' from Yersinia enterocolitica species, where this virulence protein was identified. In bacterial pathogenesis, Yop effector proteins are translocated into the eukaryotic cells.
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Protein Domain
IPR029778 | CEP85L
Type: Family
Description: Centrosomal protein of 85kDa-like (CEP85L) may localise to the centrosome []. It is also known as breast cancer antigen NY-BR-15 []. A chromosomal aberration involving CEP85L was found in a patient with T-lymphoblastic lymphoma and associated myeloproliferative neoplasm [].
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Protein Domain
IPR030887 | OMP_YaiO_dom
Type: Domain
Description: Proteins in this entry share a domain of bacterial outer membrane beta barrel, up to the protein C-terminal residue (usually Phe or Trp). The member YaiO was experimentally shown to be localised to the outer membrane [].
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Protein Domain
IPR029744 | SPATA2
Type: Family
Description: Spermatogenesis-associated protein 2 (SPATA2 or PD1) was isolated in testis, suggesting a role in the regulation of spermatogenesis []. More recent evidence indicates that this protein may have a broader function [], including a role in pancreatic beta-cell function [].
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Protein Domain
IPR005901 | GLPGLI
Type: Family
Description: This protein family was first noted as a paralogous set in Porphyromonas gingivalis, but it is more widely distributed among the Bacteroidetes. The protein family is now renamed GLPGLI after its best-conserved motif.
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Protein Domain
IPR037042 | YdaT_toxin_sf
Type: Homologous_superfamily
Description: YdaT toxin was first thought to be neutralised by the putative antitoxin YdaS () []but recent studies showed that both YdaS and YdaT can act independently as toxins and are regulated by RacR [].
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Protein Domain
IPR025261 | DUF4210
Type: Domain
Description: The function of this domain is not known. Proteins containing this domain includes the animal FAM214 proteins and the fission yeast SPAC3H8.04 protein. From a high-throughput knockout screen, SPAC3H8.04 was identified as a protein required for meiotic chromosome segregation [].
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Protein Domain
IPR025288 | DUF4080
Type: Domain
Description: This presumed domain is found at the C terminus of a number of sequences annotated as radical SAM methylthiotransferases. The domain is functionally uncharacterised. It was found by clustering human gut metagenomic sequences [].
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Protein Domain
IPR025750 | DPF1-3_N
Type: Domain
Description: This putative domain has been detected on requiem/DPF family proteins. It was identified as an adaptor molecule that links nuclear factor kappa-light-chain-enhancer of activated B cells (NF-kappa-B) dimer RelB/p52 and switch/sucrose-nonfermentable (SWI/SNF) chromatin remodeling factor [].
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Protein Domain
IPR011692 | Stress_up-reg_Nod19
Type: Family
Description: This family of plant proteins have been implicated in nodule development []in the legume Medicago truncatula (Barrel medic). MtN-19 was shown by Northern blot to be induced during nodulation []. The molecular function of these proteins is unknown.
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Protein Domain
IPR033223 | TTMP
Type: Family
Description: TTMP (C3orf52) was identified as a gene upregulated after treatment with the potent tumour promoter TPA (12-O-Tetradecanoylphorbol-13-acetate). It encodes a single-pass transmembrane protein localized to the endoplasmic reticulum [].
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Protein Domain
IPR016368 | VapD
Type: Family
Description: This entry represents the virulence-associated protein, VapD type, found in bacteria. These proteins are defined by a conserved region found at the N terminus of the protein []. The crystal structure VapD from Helicobacter pylori, which showed endoribonuclease activity, was solved by X-ray chrystallography, showing a modified ferredoxin-like fold, very similar to that of the Cas2 family. It was also related to toxin-antitoxin (TA) systems, sltho it does not belong to them [].
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Protein Domain
IPR004191 | Integrase_Tn916-type_DNA-bd_N
Type: Domain
Description: The integrase family of site-specific recombinases catalyze a diverse array of DNA rearrangements in archaebacteria, eubacteria and yeast. The structure of theDNA binding domain of the the conjugative transposon Tn916 integrase protein was determined using NMR spectroscopy. The N-terminal domain was found to be structurally similar to the double stranded RNA binding domain (dsRBD). Experimental evidence suggests that the integrase protein interacts with DNA using residues located on the face of its three stranded β-sheet [].
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Protein Domain
IPR014379 | Pfk27
Type: Family
Description: When compared with bifunctional 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatases, members of this group show similarities only to the kinase domains (). The protein encoded by PFK27 in Saccharomyces cerevisiae was shown to be a second inducible 6-phosphofructo-2-kinase []. Expression of Pfk27 was induced by glucose and sucrose, but not by galactose or maltose, this suggests that sugar transport may be involved in triggering the induction signal [].The 6-phosphofructo-2-kinase domain () may not be detected.
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Protein Domain
IPR004886 | Glucanosyltransferase
Type: Family
Description: This is a family of yeast glycosylphosphatidylinositol-anchored beta(1-3)glucanosyltransferases []. It includes Candida albicans pH-regulated protein PHR1, which is required for apical growth and plays a role in morphogenesis []and Saccharomyces cerevisiae glycolipid anchored surface protein Gas1-5 [].Gas1 is a beta-1,3-glucanosyltransferase that was initially characterised at the cell wall where it remodels chains of beta-1,3-glucan. Later, it was found to be involved in transcriptional silencing []and DNA damage response [].
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Protein Domain
IPR026673 | SPEC3/Stum
Type: Family
Description: Proteins in this family are multi-pass membrane proteins including SPEC3 and Stum. The Stum protein was identified in Drosophila and has orthologues in animals ranging from nematodes to mammals. It is required for transduction of mechanical stimuli [].Purple sea urchin SPEC3 was found at the cilia and Golgi complexes of embryonic ectoderm cells. It has been suggested that this protein involves in ectodermal ciliogenesis [, ].
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Protein Domain
IPR033879 | UPP_Pase
Type: Domain
Description: Several members of this family have been annotated as bacitracin transport permeases, as it was suspected that they form the permease component of an ABC transporter system. It was shown, however, that BcrC from Bacillus subtilis posesses undecaprenyl pyrophosphate (UPP) phospatase activity, and it is hypothesized that it competes with bacitracin for UPP, increasing the cell's resistance to bacitracin [, ]. YbjG from E. coli may function in the recycling of periplasmic undecaprenyl pyrophosphate [].
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Protein Domain
IPR025807 | Adrift-typ_MeTrfase
Type: Domain
Description: In higher eukaryotes, including insects, vertebrates and their viruses, mRNA and snRNA 5'-ends are modified by the addition of methyl groups to the first and/or the second transcribed nucleotides. Methylation of the ribose on the second transcribed position is termed cap2, and the enzyme responsible is the cap-specific mRNA (nucleoside-2'-O-)-methyltransferase or cap methyltransferase 2 []. In Drosophila, this protein was originally known as adrift, and was isolated as a gene required for pathfinding on the segmental nerve [].
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Protein Domain
IPR013484 | MoaB_proteobac
Type: Family
Description: MoaB is thought to be involved in molybdopterin biosynthesis, though its exact role is not known. Structural studies of this polypeptide suggest that it may play a role in substrate-shuttling during biosynthesis []. MoaB was capable of binding GTP, and it was suggested that the putative active site could also bind precursor Z and/or molybdenum. Potential protein interaction domains were also found, implying that MoaB may play a transport and/or storage role in molybdopterin biosynthesis.
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Protein Domain
IPR037513 | NQO
Type: Family
Description: WrbA (tryptophan (W) repressor-binding protein) was discovered in Escherichia coli, where it was proposed to play a role in regulation of the tryptophan operon [], which has been put in question since then []. Instead, WrbA has been shown to have FMN-dependent NAD(P)H:quinone oxidoreductase acivity [, ]. A role in quinone detoxification has been proposed, supported by evidence suggesting its involvement in oxidative defense and/or cell signaling [, ].
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Protein Domain
IPR034355 | AKAP17A
Type: Family
Description: A-kinase anchor protein 17A (AKAP17A) was originally reported as the pseudoautosomal or X inactivation escape gene 7 (XE7) and as B-lymphocyte antigen precursor []. Later, AKAP17A has been suggested to be an alternative splicing factor and an SR-related splicing protein that interacts with the classical SR protein ASF/SF2 and the SR-related factor ZNF265 []. It was also found to be an A-kinase anchoring protein that targets protein kinase A to splicing factor compartments [].
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Protein Domain
IPR010206 | PolA_pol_I
Type: Family
Description: This entry describes poly(A) polymerase I (also known as PcnB and plasmid copy number protein). These enzymes sequentially add adenosine nucleotides to the 3' end of RNAs, targeting them for degradation by the cell [, ]. This was originally described for anti-sense RNAs, but was later demonstrated for mRNAs as well []. Members of this family are predominantly found in the gamma- and beta-proteobacteria, with putative members in the Chlamydiacae and Spirochetes. This family has homology to tRNA nucleotidyltransferase.
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Protein Domain
IPR001566 | 23S_rRNA_MeTrfase_RlmD
Type: Family
Description: This family represents the RlmD (also known as rumA / ygcA) RNA uridine methyltransferase. In E. coli, methyltransferases are responsible for converting uridine to thymidine in rRNA and tRNAs. Among them, TrmA is responsible for tRNA U54 methylation. RlmD (assigned as YgcA previously) was first identified as a methyltransferase through its homology to the TrmA family. RlmD was then found acting as a methyltransferase on the 23S RNA for the conserved U1939. [, ].
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Protein Domain
IPR009472 | Tab2-like
Type: Family
Description: Tab2 was first identified in Chlamydomonas reinhardtii as a RNA binding protein required for translation of the chloroplast PsaB photosystem I subunit []. Later, the Tab2 homologue from Arabidopsis was found involved in the signalling pathway of light-controlled synthesis of photosystem proteins during early plant development, that probably functions as an activator of translation with targets at PSI and PSII [, ]. Proteins in this entry are from photosynthetic organisms including plants and cyanobacteria.
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Protein Domain
IPR010776 | Hop2_WH_dom
Type: Domain
Description: Homologous-pairing protein 2 (Hop2) is required for proper homologous pairing and efficient cross-over and intragenic recombination during meiosis [, , ].The mammalian HOP2 homologue, TBPIP, was first identified as a factor interacting with TBP-1, which binds to the human immunodeficiency virus, type 1 Tat protein []. Later, TBPIP was found to be an activator that specifically stimulates the homologous pairing catalyzed by DMC1 []. This entry represents the winged helix domain found in Hop2.
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Protein Domain
IPR046760 | Tab2-like_N
Type: Domain
Description: This entry represents the N-terminal domain of proteins from photosynthetic organisms including plants and cyanobacteria, such as Tab2 proteins. Tab2 was first identified in Chlamydomonas reinhardtii as a RNA binding protein required for translation of the chloroplast PsaB photosystem I subunit []. Later, the Tab2 homologue (ATAB2) from Arabidopsis was found involved in the signalling pathway of light-controlled synthesis of photosystem proteins during early plant development [], presumably functioning as an activator of translation with targets at PSI and PSII [].
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Protein Domain
IPR007662 | SigmaC_C
Type: Domain
Description: Protein sigmaC in its native state was shown to be a homotrimer. It was demonstrated that the sigmaC subunits are not covalently bound via disulphide linkages and the formation of an intrachain disulphide bond between the two cysteine residues of the sigmaC polypeptide may have a negative effect on oligomer stability. The susceptibility of the trimer to pH, temperature, ionic strength, chemical denaturants and detergents indicates that hydrophobic interactions contribute much more to oligomer stability than do ionic interactions and hydrogen bonding [].
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Protein Domain
IPR044428 | SETD3_SET
Type: Domain
Description: This entry represents the SET domain found in SETD3 and related proteins.SETD3 is a protein-histidine N-methyltransferase that specifically mediates methylation of actin at 'His-73' []. It was initially reported to have histone methyltransferase activity and methylate 'Lys-4' and 'Lys-36' of histone H3 (H3K4me and H3K36me). However, this conclusion was based on mass spectrometry data wherein mass shifts were inconsistent with a bona fide methylation event. In vitro, the protein-lysine methyltransferase activity is weak compared to the protein-histidine methyltransferase activity [].
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Protein Domain
IPR029160 | CCSMST1_fam
Type: Family
Description: This family of proteins was discovered in a screen of Bos taurus placental ESTs. The B. taurus member of this family was named cattle cerebrum and skeletal muscle-specific transcript 1 (CCSMST1) [], hence the name of the family. This family of proteins is found in metazoa, both in vertebrates and invertebrates. Proteins are typically between 97 and 157 amino acids in length with a single completely conserved residue D that may be functionally important. Their function is unknown.
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Protein Domain
IPR019707 | DUF2582
Type: Family
Description: This domain is conserved in bacteria and archaea. The function is not known. The structure of two proteins in this family were solved using NMR and shown to adopt a winged helix-turn-helix fold []. Structural analysis shows that these proteins form an unusual dimeric conformation. This dimer was shown to be similar to that found in the FadR and TubR wHTH domains. It was suggested []that these proteins are not very likely to bind to DNA.
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Protein Domain
IPR027326 | KIF20A
Type: Family
Description: Kinesin-like protein KIF20A was first identified as a binding partner for the rab6 GTPase involved in protein transport at the Golgi apparatus []. It was later found to be a mitotic kinesin required for chromosome passenger complex (CPC)-mediated cytokinesis. It is phosphorylated by PLK1 at Ser-528 during mitosis, creating a docking site for PLK1 and recruiting PLK1 at central spindle. It contains a kinesin-motor domain and has a microtubule plus end-directed motility [].
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