cd00002, YbaK_deacylase, This CD includes cysteinyl-tRNA(Pro) deacylases from Haemophilus influenzae and Escherichia coli and other related bacterial proteins. These trans-acting, single-domain proteins are homologs of ProX and also the cis-acting prolyl-tRNA synthetase (ProRS) inserted (INS) editing domain. The bacterial amino acid trans-editing enzyme YbaK is a deacylase that hydrolyzes cysteinyl-tRNA(Pro)'s mischarged by prolyl-tRNA synthetase. YbaK also hydrolyzes glycyl-tRNA's, alanyl-tRNA's, seryl-tRNA's, and prolyl-tRNA's. YbaK is homologous to the INS domain of prolyl-tRNA synthetase (ProRS) as well as the trans-editing enzyme ProX of Aeropyrum pernix which hydrolyzes alanyl-tRNA's and glycyl-tRNA's.
pfam04365, BrnT_toxin, Ribonuclease toxin, BrnT, of type II toxin-antitoxin system. BrnT is a ribonuclease toxin of a type II toxin-antitoxin system that exhibits a RelE-like fold. The antitoxin that neutralizes this toxin is pfam14384. BrnT is found in bacteria, archaea, bacteriophage, and plasmids. BrnT-BrnA forms a 2:2 tetrameric complex and autoregulates its own expression, which is induced by a number of different environmental stresses. Expression of BrnT alone results in cessation of bacterial growth which can be rescued after subsequent expression of BrnA.
pfam01930, Cas_Cas4, Domain of unknown function DUF83. This domain has no known function. The domain contains three conserved cysteines at its C-terminus.
pfam05107, Cas_Cas7, CRISPR-associated protein Cas7. CRISPR-associated protein Cas7 is one of the components of the type I-B cascade-like antiviral defense complex. In Haloferax volcanii, Cas5, Cas6 and Cas7 form a small complex that aids the stability of CRISPR-derived RNA.
cd09725, Cas2_I_II_III, CRISPR/Cas system-associated protein Cas2. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Cas2 is present in majority of CRISPR/Cas systems along with Cas1; RNAse specific to U-rich regions; Possesses an RRM/ferredoxin fold.
cd09722, Cas1_I-B, CRISPR/Cas system-associated protein Cas1. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Cas1 is the most universal CRISPR system protein thought to be involved in spacer integration; Cas1 is metal-dependent deoxyribonuclease, also binds RNA; Shown to possess a unique fold consisting of a N-terminal beta-strand domain and a C-terminal alpha-helical domain.
pfam12441, CopG_antitoxin, CopG antitoxin of type II toxin-antitoxin system. CopG antitoxin is a member of a type II toxin-antitoxin system family found in bacteria and archaea. Most antitoxins encoded by the relBE and parDE loci belong to the MetJ/Arc/CopG family of dimeric proteins which bind DNA through N-terminal ribbon-helix-helix (RHH) motifs. The toxin for CopG proteins falls into the family BrnT_toxin, pfam04365.
pfam10442, FIST_C, FIST C domain. The FIST C domain is a novel sensory domain, which is present in signal transduction proteins from Bacteria, Archaea and Eukarya. Chromosomal proximity of FIST-encoding genes to those coding for proteins involved in amino acid metabolism and transport suggest that FIST domains bind small ligands, such as amino acids.
TIGR02592, hypothetical_protein_CTC_01466, CRISPR-associated protein Cas5, subtype I-B/HMARI. This is a CRISPR-associated protein unique to the hmari subtype of cas genes and CRISPR repeat, which is the only subtype present in Haloarcula marismortui ATCC 43049. The hmari type, though uncommon, is also found in the Aquificae, Thermotogae, Firmicutes, and Dictyoglomi.
TIGR01877, CRISPR-associated_endoribonuclease_Cas6_1, CRISPR-associated endoribonuclease Cas6. CRISPR is a term for Clustered, Regularly Interspaced Short Palidromic Repeats. A number of protein families appear only in association with these repeats and are designated Cas (CRISPR-Associated) proteins. This broadly distributed, highly divergent Cas family is now characterized as an endoribonuclease that generates guide RNAs for host defense against phage and other invaders. The family contains a C-terminal motif GXGXXXXXGXG, where the each X between two Gly is hydrophobic and the spacer XXXXX contains (usually) one Arg or Lys. The seed alignment for the current version of this model has gappy columns removed. Members of this protein family are found associated with several different CRISPR/cas system subtypes, and consequently we designate this family Cas6.
pfam12913, SH3_6, SH3 domain (SH3b1 type). This domain appears to be an SH3 domain of the SH3b1-type, and is just C-terminal to an N-terminal domain that is probably the stabilizing domain for the structure from Desulfovibrio vulgaris DVU_0896, Structure 3m1u, which is a four-domain protein. The next domain is an SH3b2 and the last, the C-terminal region, is the catalytic domain of the cysteine-peptidase type, ie family NLPC_P60, pfam00877 (details derived from TOPSAN).
cd18037, DEXSc_Pif1_like, DEAD-box helicase domain of Pif1. Pif1 and other members of this family are RecD-like helicases involved in maintaining genome stability through unwinding double-stranded DNAs (dsDNAs), DNA/RNA hybrids, and G quadruplex (G4) structures. The members of Pif1 helicase subfamily studied so far all appear to contribute to telomere maintenance. Pif1 is a member of the DEAD-like helicases superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
sd00006, TPR, Tetratricopeptide repeat. The Tetratricopeptide repeat (TPR) typically contains 34 amino acids and is found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans. It is present in a variety of proteins including those involved in chaperone, cell-cycle, transcription, and protein transport complexes. The number of TPR motifs varies among proteins. Those containing 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accommodate an alpha-helix of a target protein. It has been proposed that TPR proteins preferentially interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes.
cd17534, REC_DC-like, phosphoacceptor receiver (REC) domain of modulated diguanylate cyclase and similar domains. This groups includes a modulated diguanylate cyclase containing a PAS sensor domain from Desulfovibrio desulfuricans G20. Members of this group contain N-terminal REC domains and various output domains including the GGDEF, histidine kinase, and helix-turn-helix (HTH) DNA binding domains. Also included in this family is Mycobacterium tuberculosis PdtaR, a transcriptional antiterminator that contains a REC domain and an ANTAR RNA-binding output domain. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.
cd07989, LPLAT_AGPAT-like, Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like. Lysophospholipid acyltransferase (LPLAT) superfamily member: acyltransferases of de novo and remodeling pathways of glycerophospholipid biosynthesis which catalyze the incorporation of an acyl group from either acylCoAs or acyl-acyl carrier proteins (acylACPs) into acceptors such as glycerol 3-phosphate, dihydroxyacetone phosphate or lyso-phosphatidic acid. Included in this subgroup are such LPLATs as 1-acyl-sn-glycerol-3-phosphate acyltransferase (AGPAT, PlsC), Tafazzin (product of Barth syndrome gene), and similar proteins.
cd00009, AAA, The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases.
cd01007, PBP2_BvgS_HisK_like, The type 2 periplasmic ligand-binding protein domain of the sensor-kinase BvgS and histidine kinase receptors, and related proteins. This family comprises the periplasmic sensor domain of the two-component sensor-kinase systems, such as the sensor protein BvgS of Bordetella pertussis and histidine kinase receptors (HisK), and uncharacterized related proteins. Typically, the two-component system consists of a membrane spanning sensor-kinase and a cytoplasmic response regulator. It serves as a stimulus-response coupling mechanism to enable microorganisms to sense and respond to changes in environmental conditions. The N-terminal sensing domain of the sensor kinase detects extracellular signals, such as small molecule ligands and ions, which then modulate the catalytic activity of the cytoplasmic kinase domain through a phosphorylation cascade. The periplasmic sensor domain belongs to the type 2 periplasmic-binding fold protein (PBP2) superfamily, whose members are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor. PBP2 typically comprises of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two receptor cytoplasmically-located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.
TIGR03346, chaperone_ClpB, ATP-dependent chaperone ClpB. Members of this protein family are the bacterial ATP-dependent chaperone ClpB. This protein belongs to the AAA family, ATPases associated with various cellular activities (pfam00004). This molecular chaperone does not act as a protease, but rather serves to disaggregate misfolded and aggregated proteins. [Protein fate, Protein folding and stabilization].
The bacterium proteins that are colored denote the protein is present at specific phage-related keywords (such as 'capsid', 'head', 'integrase', 'plate', 'tail', 'fiber', 'coat', 'transposase', 'portal', 'terminase', 'protease' or 'lysin' and 'tRNA')
