Protein Family Models

Family members include OrfA protein, a multifunctional accessory protein found in Feline immunodeficiency virus (FIV), a lentivirus that causes AIDS in domestic cats [1]. Multiple potential functions have been ascribed to OrfA, including transactivation of viral protein expression [2], effects on virion formation and infectivity [3], host cell cycle arrest [4] and downregulation of cell surface expression of the primary FIV receptor, CD134 [5]. [1]. 23658451. Accessory genes confer a high replication rate to virulent. feline immunodeficiency virus.. Troyer RM, Thompson J, Elder JH, VandeWoude S;. J Virol. 2013;87:7940-7951.. [2]. 9847366. Demonstration that orf2 encodes the feline immunodeficiency. virus transactivating (Tat) protein and characterization of a. unique gene product with partial rev activity.. de Parseval A, Elder JH;. J Virol. 1999;73:608-617.. [3]. 12885901. Feline immunodeficiency virus ORF-Ais required for virus. particle formation and virus infectivity.. Gemeniano MC, Sawai ET, Leutenegger CM, Sparger EE;. J Virol. 2003;77:8819-8830.. [4]. 15246256. Feline immunodeficiency virus Orf-A localizes to the nucleus and. induces cell cycle arrest.. Gemeniano MC, Sawai ET, Sparger EE;. Virology. 2004;325:167-174.. [5]. 20463078. OrfA downregulates feline immunodeficiency virus primary. receptor CD134 on the host cell surface and is important in. viral infection.. Hong Y, Fink E, Hu QY, Kiosses WB, Elder JH;. J Virol. 2010;84:7225-7232. (from Pfam)

Date:

2024-08-14

Jiv90 is a fragment of the DnaJ protein in eukaryotes and in J-domain protein interacting with viral protein (Jiv) located in the N terminal region of the pestivirus viral polypeptide. The viral protein interacts stably with non structural (NS) protein NS2, causing a conformational change in NS2-NS3 and stimulates NS2-NS3 cleavage in trans. Cleavage of NS2-NS3 increases cytopathogenicity and consequently aids viral replication. Jiv therefore acts as a regulating cofactor for NS2 auto-protease. The efficient release of NS3 from the viral polypeptide by Jiv is considered crucial to the pestivirus cytopathogenicity [1]. In eukaryotes, it usually lies 40 residues downstream of DnaJ family Pfam:PF00226. However, the function in eukaryotes is still unknown. [1]. 12970452. Cell-derived sequences in the N-terminal region of the. polyprotein of a cytopathogenic pestivirus.. Muller A, Rinck G, Thiel HJ, Tautz N;. J Virol. 2003;77:10663-10669.. [2]. 11533209. A cellular J-domain protein modulates polyprotein processing and. cytopathogenicity of a pestivirus.. Rinck G, Birghan C, Harada T, Meyers G, Thiel HJ, Tautz N;. J Virol. 2001;75:9470-9482. (from Pfam)

Date:

2024-08-14

HGAL is a family of mammalian sequences typically between 104 and 179 amino acids in length. Members were discovered in a search for proteins precipitating diffuse large B-cell lymphomas [1,2]. HGAL interacts with the cytoskeleton and aids the activity of interleukin-6 on cell migration [3]. It also modulates the RhoA signalling pathway [4]. [1]. 12509382. HGAL is a novel interleukin-4-inducible gene that strongly. predicts survival in diffuse large B-cell lymphoma.. Lossos IS, Alizadeh AA, Rajapaksa R, Tibshirani R, Levy R;. Blood. 2003;101:433-440.. [2]. 12819018. Two newly characterized germinal center B-cell-associated genes,. GCET1 and GCET2, have differential expression in normal and. neoplastic B cells.. Pan Z, Shen Y, Du C, Zhou G, Rosenwald A, Staudt LM, Greiner TC,. McKeithan TW, Chan WC;. Am J Pathol. 2003;163:135-144.. [3]. 17823310. HGAL, a lymphoma prognostic biomarker, interacts with the. cytoskeleton and mediates the effects of IL-6 on cell migration.. Lu X, Chen J, Malumbres R, Cubedo Gil E, Helfman DM, Lossos IS;. Blood. 2007;110:4268-4277.. [4]. 20844236. HGAL, a germinal center specific protein, decreases lymphoma. cell motility by modulation of the RhoA signaling pathway.. Jiang X, Lu X, McNamara G, Liu X, Cubedo E, Sarosiek KA,. Sanchez-Garcia I, Helfman DM, Lossos IS;. Blood. 2010;116:5217-5227. (from Pfam)

Date:

2024-08-14

This the envelope protein from the ssRNA GB virus genotype C. [1]. 16791024. GB virus C genotype 1 is rarely transmitted vertically but. acquired during infancy in West Africa.. Li C, Danso K, Addo-Yobo E, Dompreh A, Sarkodie F, Owusu-Ofori. S, Allain JP;. AIDS. 2006;20:1458-1460. (from Pfam)

Date:

2024-08-14

This entry is of proteins of approximately 600 residues in length containing alternating regions of conservation and low complexity. The Arabidopsis protein is a replisome factor found to bind with the mini-chromosome maintenance, MCM-binding, complex and is crucial for efficient DNA replication. The family now spans the full-length proteins. [1]. 20090939. The MCM-binding protein ETG1 aids sister chromatid cohesion. required for postreplicative homologous recombination repair.. Takahashi N, Quimbaya M, Schubert V, Lammens T, Vandepoele K,. Schubert I, Matsui M, Inze D, Berx G, De Veylder L;. PLoS Genet. 2010;6:e1000817. (from Pfam)

Date:

2024-08-14

This protein family includes two copies of a five residue motif is found in a number of bacterial proteins bearing similarity to the protein CpxP (Swiss:P32158). This is a periplasmic protein that aids in combating extracytoplasmic protein-mediated toxicity, and may also be involved in the response to alkaline pH [1]. Another member of this family, Spy (Swiss:P77754) is also a periplasmic protein that may be involved in the response to stress [2]. The homology between CpxP and Spy may indicate that these two proteins are functionally related [1]. [1]. 9473036. CpxP, a stress-combative member of the Cpx regulon.. Danese PN, Silhavy TJ;. J Bacteriol 1998;180:831-839.. [2]. 9068658. A new periplasmic protein of Escherichia coli which is. synthesized in spheroplasts but not in intact cells.. Hagenmaier S, Stierhof YD, Henning U;. J Bacteriol 1997;179:2073-2076.. [3]. 20799348. The crystal structure Escherichia coli Spy.. Kwon E, Kim DY, Gross CA, Gross JD, Kim KK;. Protein Sci. 2010; [Epub ahead of print] (from Pfam)

Date:

2024-08-14

CRISPR-associated protein Cas7 is one of the components of the type I-B cascade-like antiviral defence complex. In Haloferax volcanii, Cas5, Cas6 and Cas7 form a small complex that aids the stability of CRISPR-derived RNA [1]. [1]. 24459147. A complex of Cas proteins 5, 6, and 7 is required for the. biogenesis and stability of clustered regularly interspaced. short palindromic repeats (crispr)-derived rnas (crrnas) in. Haloferax volcanii.. Brendel J, Stoll B, Lange SJ, Sharma K, Lenz C, Stachler AE,. Maier LK, Richter H, Nickel L, Schmitz RA, Randau L, Allers T,. Urlaub H, Backofen R, Marchfelder A;. J Biol Chem. 2014;289:7164-7177. (from Pfam)

Date:

2024-08-14

These peptidases are found in Archaea and Bacteria. The example in Lactococcus lactis, PepA, aids growth on milk [1]. Pyrococcus horikoshii contain a thermostable de-blocking aminopeptidase member of this family used commercially for N-terminal protein sequencing [2]. [1]. 8535515. A non-essential glutamyl aminopeptidase is required for optimal. growth of Lactococcus lactis MG1363 in milk.. l'Anson KJ, Movahedi S, Griffin HG, Gasson MJ, Mulholland F;. Microbiology 1995;141:2873-2881.. [2]. 11798173. Active site of deblocking aminopeptidase from Pyrococcus. horikoshii.. Onoe S, Ando S, Ataka M, Ishikawa K;. Biochem Biophys Res Commun 2002;290:994-997.. [3]. 10218575. Thermostable aminopeptidase from Pyrococcus horikoshii.. Ando S, Ishikawa K, Ishida H, Kawarabayasi Y, Kikuchi H, Kosugi. Y;. FEBS Lett 1999;447:25-28.. [4]. 11980710. Tetrahedral aminopeptidase: a novel large protease complex from. archaea.. Franzetti B, Schoehn G, Hernandez JF, Jaquinod M, Ruigrok RW,. Zaccai G;. EMBO J 2002;21:2132-2138. (from Pfam)

Date:

2024-08-14

This family was first named TPM domain after its founding proteins: TLP18.3, Psb32 and MOLO-1. In Arabidopsis, this domain is called the thylakoid acid phosphatase -TAP - domain and has a Rossmann-like fold [1]. In plants, the family resides in the thylakoid lumen attached to the outer membrane of the chloroplast/plastid. It is active in the photosystem II [2,3]. [1]. 21908686. Structural and Functional Assays of AtTLP18.3 Identify Its Novel. Acid Phosphatase Activity in Thylakoid Lumen.. Wu HY, Liu MS, Lin TP, Cheng YS;. Plant physiol. 2011;9:0-0.. [2]. 17576201. TLP18.3, a novel thylakoid lumen protein regulating photosystem. II repair cycle.. Sirpio S, Allahverdiyeva Y, Suorsa M, Paakkarinen V, Vainonen J,. Battchikova N, Aro EM;. Biochem J. 2007;406:415-425.. [3]. 21653280. The Psb32 protein aids in repairing photodamaged photosystem II. in the cyanobacterium Synechocystis 6803.. Wegener KM, Bennewitz S, Oelmuller R, Pakrasi HB;. Mol Plant. 2011;4:1052-1061. (from Pfam)

Date:

2024-08-14

The matrix protein, p15, is encoded by the gag gene. MA is involved in pathogenicity [1]. [1]. 7690416. The MA (p15) and p12 regions of the gag gene are sufficient for. the pathogenicity of the murine AIDS virus.. Pozsgay JM, Beilharz MW, Wines BD, Hess AD, Pitha PM;. J Virol 1993;67:5989-5999. (from Pfam)

Date:

2024-08-14

The signal recognition particle (SRP) binds to the signal peptide of proteins as they are being translated. The binding of the SRP halts translation and the complex is then transported to the endoplasmic reticulum's cytoplasmic surface. The SRP then aids translocation of the protein through the ER membrane. The SRP is a ribonucleoprotein that is composed of a small RNA and several proteins. One of these proteins is the SRP19 protein [1] (Sec65 in yeast [2,3]). [1]. 2460823. Isolation and characterization of a cDNA clone encoding the 19. kDa protein of signal recognition particle (SRP): expression and. binding to 7SL RNA.. Lingelbach K, Zwieb C, Webb JR, Marshallsay C, Hoben PJ, Walter. P, Dobberstein B;. Nucleic Acids Res 1988;16:9431-9442.. [2]. 1313947. SEC65 gene product is a subunit of the yeast signal recognition. particle required for its integrity.. Hann BC, Stirling CJ, Walter P;. Nature 1992;356:532-533.. [3]. 1313948. The S. cerevisiae SEC65 gene encodes a component of yeast signal. recognition particle with homology to human SRP19.. Stirling CJ, Hewitt EW;. Nature 1992;356:534-537. (from Pfam)

Date:

2024-08-14

Along with the structurally unrelated Sec14p family (found in Pfam:PF00650), this family can bind/exchange one molecule of phosphatidylinositol (PI) or phosphatidylcholine (PC) and thus aids their transfer between different membrane compartments. There are three sub-families - all share an N-terminal PITP-like domain, whose sequence is highly conserved. It is described as consisting of three regions. The N-terminal region is thought to bind the lipid and contains two helices and an eight-stranded, mostly antiparallel beta-sheet. An intervening loop region, which is thought to play a role in protein-protein interactions, separates this from the C-terminal region, which exhibits the greatest sequence variation and may be involved in membrane binding. PITP alpha (Swiss:Q00169) has a 16-fold greater affinity for PI than PC. Together with PITP beta (Swiss:P48739), it is expressed ubiquitously in all tissues [1]. [1]. 11574064. The PITP family of phosphatidylinositol transfer proteins.. Hsuan J, Cockcroft S;. Genome Biol 2001;2:REVIEWS3011. (from Pfam)

Date:

2024-08-14

The retroviral p12 is a virion structural protein. p12 is proline rich. The function carried out by p12 in assembly and replication is unknown. p12 is associated with pathogenicity of the virus [1]. [1]. 7690416. The MA (p15) and p12 regions of the gag gene are sufficient for. the pathogenicity of the murine AIDS virus.. Pozsgay JM, Beilharz MW, Wines BD, Hess AD, Pitha PM;. J Virol 1993;67:5989-5999. (from Pfam)

Date:

2024-08-14

Nef protein accelerates virulent progression of AIDS by its interaction with cellular proteins involved in signal transduction and host cell activation. Nef has been shown to bind specifically to a subset of the Src kinase family. [1]. 9351809. The crystal structure of HIV-1 Nef protein bound to the Fyn. kinase SH3 domain suggests a role for this complex in altered T. cell receptor signalling. Arold S, Franken P, Strub M-P, Hoh F, Benichou S, Benarous R,. Dumas C;. Structure 1997;5:1361-1372. (from Pfam)

Date:

2024-08-14

ATP-binding cassette domain-containing protein, similar to ATP-binding protein Uup, may contain the C-terminal domain (CTD) found in ABC transporters, which aids in DNA binding

Date:

2023-09-01

SaoP, one of the nine proteins of the SAO (selenocysteine-associated organometallic) locus, is nearly always a selenoprotein, and is one of six novel selenoprotein families from that locus. The Sec (U) residue occurs at a position described in other ABC transporter permease homodimers as the channel-gating position. A role in importing (and perhaps even forming) organometallic compounds, in a cycle in which the metal atom is reexported and reused, as a cofactor that aids in utilization of some otherwise refractory substrate, has been suggested. The SAO system occurs in Clostridium difficile (a human gut pathogen), Brachyspira pilosicoli (an intestinal spirochete in chicken), Desulfopila aestuarii (a deltaproteobacterial sulfate reducer from estuary sediment), etc.

Gene:

saoP

Date:

2023-01-05

phosphatidylinositol transfer family protein may bind/exchange one molecule of phosphatidylinositol (PI) or phosphatidylcholine (PC) and thus aids their transfer between different membrane compartments

Date:

2022-01-27

protein Nef accelerates virulent progression of AIDS by its interaction with cellular proteins involved in signal transduction and host cell activation; it binds specifically to a subset of the Src kinase family

Date:

2017-05-26

AcfA (accessory colonization factor A), as discussed in Vibrio cholerae, is a porin-like outer membrane beta-barrel protein. It encoded in a locus with other proteins also termed accessory colonization factor, near the toxin-coregulated pilus genes, and its presence aids in intestinal colonization, but its molecular function is unknown. Members of the broader family, described by this HMM, are found in many species of Vibrio, Photobacterium, Aliivibrio, and related genera. The name AcfA is used also for a member of this family from Vibrio alginolyticus, that is no more than 40 percent identical in amino acid sequence, but it is unclear that all members of this family should be considered AcfA.

Date:

2020-10-26

phosphatidylinositol transfer family protein may bind/exchange one molecule of phosphatidylinositol (PI) or phosphatidylcholine (PC) and thus aids their transfer between different membrane compartments

Date:

2023-01-19