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EEC98443.1 EEC98443.1 alaS alaS ksgA ksgA rsgA rsgA rnr rnr dtd dtd csn1 csn1 rnpA rnpA tyrS tyrS EEC97905.1 EEC97905.1 rnc rnc metG metG rpsO rpsO EEC97703.1 EEC97703.1 pnp pnp thrS thrS rho rho ffh ffh EEC96221.1 EEC96221.1 EEC96191.1 EEC96191.1 rpsD rpsD rpsK rpsK rpsM rpsM infA infA rplO rplO rpsE rpsE rplR rplR rplF rplF rpsH rpsH rpsN rpsN rplE rplE rplX rplX rplN rplN rpsQ rpsQ rplP rplP rpsC rpsC EEC96155.1 EEC96155.1 rplV rplV rpsS rpsS rplB rplB rplW rplW rplD rplD rplC rplC rpsG rpsG rpsL rpsL era era pheT pheT nusB nusB rplU rplU rplY rplY EEC95765.1 EEC95765.1 rny rny smpB smpB EEC95566.1 EEC95566.1 EEC95315.1 EEC95315.1 rplI rplI rpsR rpsR rpsF rpsF rplA rplA rplK rplK EEC94604.1 EEC94604.1 rpsT rpsT nusA nusA EEC94288.1 EEC94288.1
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query proteins and first shell of interactors
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second shell of interactors
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proteins of unknown 3D structure
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a 3D structure is known or predicted
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EEC98443.1Putative ribosomal protein S1; Binds mRNA; thus facilitating recognition of the initiation point. It is needed to translate mRNA with a short Shine-Dalgarno (SD) purine-rich sequence. (597 aa)
alaSalanine--tRNA ligase; Catalyzes the attachment of alanine to tRNA(Ala) in a two- step reaction: alanine is first activated by ATP to form Ala-AMP and then transferred to the acceptor end of tRNA(Ala). Also edits incorrectly charged Ser-tRNA(Ala) and Gly-tRNA(Ala) via its editing domain. (875 aa)
ksgADimethyladenosine transferase; Specifically dimethylates two adjacent adenosines (A1518 and A1519) in the loop of a conserved hairpin near the 3'-end of 16S rRNA in the 30S particle. May play a critical role in biogenesis of 30S subunits. (290 aa)
rsgARibosome small subunit-dependent GTPase A; One of several proteins that assist in the late maturation steps of the functional core of the 30S ribosomal subunit. Helps release RbfA from mature subunits. May play a role in the assembly of ribosomal proteins into the subunit. Circularly permuted GTPase that catalyzes slow GTP hydrolysis, GTPase activity is stimulated by the 30S ribosomal subunit; Belongs to the TRAFAC class YlqF/YawG GTPase family. RsgA subfamily. (310 aa)
rnrRibonuclease R; 3'-5' exoribonuclease that releases 5'-nucleoside monophosphates and is involved in maturation of structured RNAs. (726 aa)
dtdD-tyrosyl-tRNA(Tyr) deacylase; An aminoacyl-tRNA editing enzyme that deacylates mischarged D-aminoacyl-tRNAs. Also deacylates mischarged glycyl-tRNA(Ala), protecting cells against glycine mischarging by AlaRS. Acts via tRNA- based rather than protein-based catalysis; rejects L-amino acids rather than detecting D-amino acids in the active site. By recycling D- aminoacyl-tRNA to D-amino acids and free tRNA molecules, this enzyme counteracts the toxicity associated with the formation of D-aminoacyl- tRNA entities in vivo and helps enforce protein L-homochirality. Belongs to the DTD family. (150 aa)
csn1CRISPR-associated protein, Csn1 family; CRISPR (clustered regularly interspaced short palindromic repeat) is an adaptive immune system that provides protection against mobile genetic elements (viruses, transposable elements and conjugative plasmids). CRISPR clusters contain spacers, sequences complementary to antecedent mobile elements, and target invading nucleic acids. CRISPR clusters are transcribed and processed into CRISPR RNA (crRNA). In type II CRISPR systems correct processing of pre-crRNA requires a trans- encoded small RNA (tracrRNA), endogenous ribonuclease 3 (rnc) and this [...] (1443 aa)
rnpAPutative ribonuclease P protein component; RNaseP catalyzes the removal of the 5'-leader sequence from pre-tRNA to produce the mature 5'-terminus. It can also cleave other RNA substrates such as 4.5S RNA. The protein component plays an auxiliary but essential role in vivo by binding to the 5'-leader sequence and broadening the substrate specificity of the ribozyme. (128 aa)
tyrStyrosine--tRNA ligase; Catalyzes the attachment of tyrosine to tRNA(Tyr) in a two- step reaction: tyrosine is first activated by ATP to form Tyr-AMP and then transferred to the acceptor end of tRNA(Tyr); Belongs to the class-I aminoacyl-tRNA synthetase family. TyrS type 1 subfamily. (430 aa)
EEC97905.1THUMP domain protein; KEGG: fnu:FN0344 4.6e-56 methyltransferase K07444; Psort location: Cytoplasmic, score: 8.96; Belongs to the methyltransferase superfamily. (506 aa)
rncRibonuclease III; Digests double-stranded RNA. Involved in the processing of primary rRNA transcript to yield the immediate precursors to the large and small rRNAs (23S and 16S). Processes some mRNAs, and tRNAs when they are encoded in the rRNA operon. Processes pre-crRNA and tracrRNA of type II CRISPR loci if present in the organism. (286 aa)
metGmethionine--tRNA ligase; Is required not only for elongation of protein synthesis but also for the initiation of all mRNA translation through initiator tRNA(fMet) aminoacylation. (679 aa)
rpsORibosomal protein S15; Forms an intersubunit bridge (bridge B4) with the 23S rRNA of the 50S subunit in the ribosome. (89 aa)
EEC97703.1S4 domain protein; KEGG: sec:SC4072 1.5e-13 yjbC; putative pseudouridine synthase K06182. (201 aa)
pnpPolyribonucleotide nucleotidyltransferase; Involved in mRNA degradation. Catalyzes the phosphorolysis of single-stranded polyribonucleotides processively in the 3'- to 5'- direction. (743 aa)
thrSthreonine--tRNA ligase; Catalyzes the attachment of threonine to tRNA(Thr) in a two- step reaction: L-threonine is first activated by ATP to form Thr-AMP and then transferred to the acceptor end of tRNA(Thr). (651 aa)
rhoTranscription termination factor Rho; Facilitates transcription termination by a mechanism that involves Rho binding to the nascent RNA, activation of Rho's RNA- dependent ATPase activity, and release of the mRNA from the DNA template. (682 aa)
ffhSignal recognition particle protein; Involved in targeting and insertion of nascent membrane proteins into the cytoplasmic membrane. Binds to the hydrophobic signal sequence of the ribosome-nascent chain (RNC) as it emerges from the ribosomes. The SRP-RNC complex is then targeted to the cytoplasmic membrane where it interacts with the SRP receptor FtsY. Belongs to the GTP-binding SRP family. SRP54 subfamily. (441 aa)
EEC96221.1tRNA nucleotidyltransferase/poly(A) polymerase family protein; KEGG: bth:BT1975 3.0e-194 tRNA nucleotidyltransferase K00970; Psort location: Cytoplasmic, score: 8.96; Belongs to the tRNA nucleotidyltransferase/poly(A) polymerase family. (476 aa)
EEC96191.1NOL1/NOP2/sun family protein; KEGG: spa:M6_Spy0946 5.0e-50 putative 23S rRNA m(5)C methyltransferase K00599; Psort location: Cytoplasmic, score: 8.96. (467 aa)
rpsDRibosomal protein S4; One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the body of the 30S subunit. (201 aa)
rpsK30S ribosomal protein S11; Located on the platform of the 30S subunit, it bridges several disparate RNA helices of the 16S rRNA. Forms part of the Shine- Dalgarno cleft in the 70S ribosome; Belongs to the universal ribosomal protein uS11 family. (129 aa)
rpsM30S ribosomal protein S13; Located at the top of the head of the 30S subunit, it contacts several helices of the 16S rRNA. In the 70S ribosome it contacts the 23S rRNA (bridge B1a) and protein L5 of the 50S subunit (bridge B1b), connecting the 2 subunits; these bridges are implicated in subunit movement. Contacts the tRNAs in the A and P-sites. Belongs to the universal ribosomal protein uS13 family. (126 aa)
infATranslation initiation factor IF-1; One of the essential components for the initiation of protein synthesis. Stabilizes the binding of IF-2 and IF-3 on the 30S subunit to which N-formylmethionyl-tRNA(fMet) subsequently binds. Helps modulate mRNA selection, yielding the 30S pre-initiation complex (PIC). Upon addition of the 50S ribosomal subunit IF-1, IF-2 and IF-3 are released leaving the mature 70S translation initiation complex. (72 aa)
rplORibosomal protein L15; Binds to the 23S rRNA; Belongs to the universal ribosomal protein uL15 family. (148 aa)
rpsERibosomal protein S5; Located at the back of the 30S subunit body where it stabilizes the conformation of the head with respect to the body. Belongs to the universal ribosomal protein uS5 family. (174 aa)
rplRRibosomal protein L18; This is one of the proteins that binds and probably mediates the attachment of the 5S RNA into the large ribosomal subunit, where it forms part of the central protuberance. (114 aa)
rplFRibosomal protein L6; This protein binds to the 23S rRNA, and is important in its secondary structure. It is located near the subunit interface in the base of the L7/L12 stalk, and near the tRNA binding site of the peptidyltransferase center; Belongs to the universal ribosomal protein uL6 family. (183 aa)
rpsHRibosomal protein S8; One of the primary rRNA binding proteins, it binds directly to 16S rRNA central domain where it helps coordinate assembly of the platform of the 30S subunit; Belongs to the universal ribosomal protein uS8 family. (131 aa)
rpsNRibosomal protein S14p/S29e; Binds 16S rRNA, required for the assembly of 30S particles and may also be responsible for determining the conformation of the 16S rRNA at the A site; Belongs to the universal ribosomal protein uS14 family. (89 aa)
rplERibosomal protein L5; This is 1 of the proteins that binds and probably mediates the attachment of the 5S RNA into the large ribosomal subunit, where it forms part of the central protuberance. In the 70S ribosome it contacts protein S13 of the 30S subunit (bridge B1b), connecting the 2 subunits; this bridge is implicated in subunit movement. Contacts the P site tRNA; the 5S rRNA and some of its associated proteins might help stabilize positioning of ribosome-bound tRNAs. (185 aa)
rplXRibosomal protein L24; One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit. (106 aa)
rplNRibosomal protein L14; Binds to 23S rRNA. Forms part of two intersubunit bridges in the 70S ribosome; Belongs to the universal ribosomal protein uL14 family. (121 aa)
rpsQ30S ribosomal protein S17; One of the primary rRNA binding proteins, it binds specifically to the 5'-end of 16S ribosomal RNA. (85 aa)
rplPRibosomal protein L16; Binds 23S rRNA and is also seen to make contacts with the A and possibly P site tRNAs; Belongs to the universal ribosomal protein uL16 family. (144 aa)
rpsCRibosomal protein S3; Binds the lower part of the 30S subunit head. Binds mRNA in the 70S ribosome, positioning it for translation; Belongs to the universal ribosomal protein uS3 family. (244 aa)
EEC96155.1Ribosomal protein L22p/L17e. (71 aa)
rplV50S ribosomal protein L22. (61 aa)
rpsSRibosomal protein S19; Protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA. (89 aa)
rplBRibosomal protein L2; One of the primary rRNA binding proteins. Required for association of the 30S and 50S subunits to form the 70S ribosome, for tRNA binding and peptide bond formation. It has been suggested to have peptidyltransferase activity; this is somewhat controversial. Makes several contacts with the 16S rRNA in the 70S ribosome. Belongs to the universal ribosomal protein uL2 family. (274 aa)
rplWRibosomal protein L23; One of the early assembly proteins it binds 23S rRNA. One of the proteins that surrounds the polypeptide exit tunnel on the outside of the ribosome. Forms the main docking site for trigger factor binding to the ribosome; Belongs to the universal ribosomal protein uL23 family. (97 aa)
rplD50S ribosomal protein L4; Forms part of the polypeptide exit tunnel. (209 aa)
rplC50S ribosomal protein L3; One of the primary rRNA binding proteins, it binds directly near the 3'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit; Belongs to the universal ribosomal protein uL3 family. (205 aa)
rpsGRibosomal protein S7; One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the head domain of the 30S subunit. Is located at the subunit interface close to the decoding center, probably blocks exit of the E-site tRNA; Belongs to the universal ribosomal protein uS7 family. (158 aa)
rpsLRibosomal protein S12; Interacts with and stabilizes bases of the 16S rRNA that are involved in tRNA selection in the A site and with the mRNA backbone. Located at the interface of the 30S and 50S subunits, it traverses the body of the 30S subunit contacting proteins on the other side and probably holding the rRNA structure together. The combined cluster of proteins S8, S12 and S17 appears to hold together the shoulder and platform of the 30S subunit. (136 aa)
eraRibosome biogenesis GTPase Era; An essential GTPase that binds both GDP and GTP, with rapid nucleotide exchange. Plays a role in 16S rRNA processing and 30S ribosomal subunit biogenesis and possibly also in cell cycle regulation and energy metabolism. (296 aa)
pheTphenylalanine--tRNA ligase, beta subunit; KEGG: bfs:BF2590 0. putative phenylalanyl-tRNA synthetase beta chain K01890; Psort location: Cytoplasmic, score: 9.97. (820 aa)
nusBTranscription antitermination factor NusB; Involved in transcription antitermination. Required for transcription of ribosomal RNA (rRNA) genes. Binds specifically to the boxA antiterminator sequence of the ribosomal RNA (rrn) operons. (308 aa)
rplURibosomal protein L21; This protein binds to 23S rRNA in the presence of protein L20; Belongs to the bacterial ribosomal protein bL21 family. (105 aa)
rplYRibosomal protein L25, Ctc-form; This is one of the proteins that binds to the 5S RNA in the ribosome where it forms part of the central protuberance. Belongs to the bacterial ribosomal protein bL25 family. CTC subfamily. (194 aa)
EEC95765.1S4 domain protein; Psort location: Cytoplasmic, score: 8.96. (144 aa)
rnyYmdA/YtgF family protein; Endoribonuclease that initiates mRNA decay. Belongs to the RNase Y family. (511 aa)
smpBSsrA-binding protein; Required for rescue of stalled ribosomes mediated by trans- translation. Binds to transfer-messenger RNA (tmRNA), required for stable association of tmRNA with ribosomes. tmRNA and SmpB together mimic tRNA shape, replacing the anticodon stem-loop with SmpB. tmRNA is encoded by the ssrA gene; the 2 termini fold to resemble tRNA(Ala) and it encodes a 'tag peptide', a short internal open reading frame. During trans-translation Ala-aminoacylated tmRNA acts like a tRNA, entering the A-site of stalled ribosomes, displacing the stalled mRNA. The ribosome then switches to [...] (154 aa)
EEC95566.1KEGG: chu:CHU_3712 9.5e-88 hypothetical protein K00599. (394 aa)
EEC95315.1Pseudouridine synthase, RluA family; Responsible for synthesis of pseudouridine from uracil. Belongs to the pseudouridine synthase RluA family. (306 aa)
rplIRibosomal protein L9; Binds to the 23S rRNA. (147 aa)
rpsRRibosomal protein S18; Binds as a heterodimer with protein S6 to the central domain of the 16S rRNA, where it helps stabilize the platform of the 30S subunit; Belongs to the bacterial ribosomal protein bS18 family. (89 aa)
rpsFRibosomal protein S6; Binds together with S18 to 16S ribosomal RNA. (117 aa)
rplARibosomal protein L1; Binds directly to 23S rRNA. The L1 stalk is quite mobile in the ribosome, and is involved in E site tRNA release. (232 aa)
rplKRibosomal protein L11; Forms part of the ribosomal stalk which helps the ribosome interact with GTP-bound translation factors. (147 aa)
EEC94604.1Pseudouridylate synthase; KEGG: bfr:BF4017 2.9e-102 ribosomal large subunit pseudouridine synthase B K06178; Psort location: Cytoplasmic, score: 8.96; Belongs to the pseudouridine synthase RsuA family. (249 aa)
rpsTRibosomal protein S20; Binds directly to 16S ribosomal RNA. (85 aa)
nusATranscription termination factor NusA; Participates in both transcription termination and antitermination. (424 aa)
EEC94288.1Pseudouridine synthase, RluA family; Responsible for synthesis of pseudouridine from uracil. Belongs to the pseudouridine synthase RluA family. (359 aa)
Your Current Organism:
Parabacteroides johnsonii
NCBI taxonomy Id: 537006
Other names: P. johnsonii DSM 18315, Parabacteroides johnsonii DSM 18315, Parabacteroides johnsonii JCM 13406, Parabacteroides johnsonii M-165, Parabacteroides johnsonii str. DSM 18315, Parabacteroides johnsonii strain DSM 18315
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