STRINGSTRING
rsmA rsmA Tint_0134 Tint_0134 rsmH rsmH rlmD rlmD obg obg Tint_0745 Tint_0745 rsgA rsgA rimM rimM Tint_1067 Tint_1067 rimP rimP rbfA rbfA rlmJ rlmJ Tint_1295 Tint_1295 Tint_1312 Tint_1312 rplT rplT rlmE rlmE Tint_1727 Tint_1727 der der rlmN rlmN Tint_1779 Tint_1779 rlmB rlmB Tint_2189 Tint_2189 rsfS rsfS rlmH rlmH era era rnc rnc Tint_2395 Tint_2395 Tint_2405 Tint_2405 rne rne Tint_2546 Tint_2546 Tint_2666 Tint_2666 rph rph ybeY ybeY Tint_2901 Tint_2901 rsmG rsmG
Nodes:
Network nodes represent proteins
splice isoforms or post-translational modifications are collapsed, i.e. each node represents all the proteins produced by a single, protein-coding gene locus.
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colored nodes:
query proteins and first shell of interactors
white nodes:
second shell of interactors
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empty nodes:
proteins of unknown 3D structure
filled nodes:
a 3D structure is known or predicted
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Edges represent protein-protein associations
associations are meant to be specific and meaningful, i.e. proteins jointly contribute to a shared function; this does not necessarily mean they are physically binding to each other.
Known Interactions
from curated databases
experimentally determined
Predicted Interactions
gene neighborhood
gene fusions
gene co-occurrence
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textmining
co-expression
protein homology
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rsmADimethyladenosine 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. (268 aa)
Tint_0134Protein of unknown function DUF558; Specifically methylates the N3 position of the uracil ring of uridine 1498 (m3U1498) in 16S rRNA. Acts on the fully assembled 30S ribosomal subunit. (236 aa)
rsmHS-adenosyl-methyltransferase MraW; Specifically methylates the N4 position of cytidine in position 1402 (C1402) of 16S rRNA. (311 aa)
rlmDRNA methyltransferase, TrmA family; Catalyzes the formation of 5-methyl-uridine at position 1939 (m5U1939) in 23S rRNA; Belongs to the class I-like SAM-binding methyltransferase superfamily. RNA M5U methyltransferase family. RlmD subfamily. (474 aa)
obgGTP-binding protein Obg/CgtA; An essential GTPase which binds GTP, GDP and possibly (p)ppGpp with moderate affinity, with high nucleotide exchange rates and a fairly low GTP hydrolysis rate. Plays a role in control of the cell cycle, stress response, ribosome biogenesis and in those bacteria that undergo differentiation, in morphogenesis control. Belongs to the TRAFAC class OBG-HflX-like GTPase superfamily. OBG GTPase family. (358 aa)
Tint_0745TIGRFAM: methyltransferase; KEGG: bvi:Bcep1808_2913 putative methyltransferase; PFAM: Protein of unknown function methylase putative. (215 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. (321 aa)
rimM16S rRNA processing protein RimM; An accessory protein needed during the final step in the assembly of 30S ribosomal subunit, possibly for assembly of the head region. Probably interacts with S19. Essential for efficient processing of 16S rRNA. May be needed both before and after RbfA during the maturation of 16S rRNA. It has affinity for free ribosomal 30S subunits but not for 70S ribosomes; Belongs to the RimM family. (180 aa)
Tint_1067TIGRFAM: ATP-dependent helicase HrpA; PFAM: helicase-associated domain protein; helicase domain protein; protein of unknown function DUF1605; KEGG: bvi:Bcep1808_2234 ATP-dependent helicase HrpA; SMART: DEAD-like helicase; AAA ATPase; helicase domain protein. (1333 aa)
rimPProtein of unknown function DUF150; Required for maturation of 30S ribosomal subunits. Belongs to the RimP family. (191 aa)
rbfARibosome-binding factor A; One of several proteins that assist in the late maturation steps of the functional core of the 30S ribosomal subunit. Associates with free 30S ribosomal subunits (but not with 30S subunits that are part of 70S ribosomes or polysomes). Required for efficient processing of 16S rRNA. May interact with the 5'-terminal helix region of 16S rRNA. (120 aa)
rlmJProtein of unknown function DUF519; Specifically methylates the adenine in position 2030 of 23S rRNA. (281 aa)
Tint_1295KEGG: lch:Lcho_1704 GTP-binding protein TypA; TIGRFAM: GTP-binding protein TypA; small GTP-binding protein; PFAM: protein synthesis factor GTP-binding; elongation factor Tu domain 2 protein; elongation factor G domain protein. (608 aa)
Tint_1312Pseudouridine synthase, RluA family; Responsible for synthesis of pseudouridine from uracil. Belongs to the pseudouridine synthase RluA family. (342 aa)
rplTRibosomal protein L20; Binds directly to 23S ribosomal RNA and is necessary for the in vitro assembly process of the 50S ribosomal subunit. It is not involved in the protein synthesizing functions of that subunit. (118 aa)
rlmERibosomal RNA methyltransferase RrmJ/FtsJ; Specifically methylates the uridine in position 2552 of 23S rRNA at the 2'-O position of the ribose in the fully assembled 50S ribosomal subunit. (216 aa)
Tint_1727PFAM: protein of unknown function UPF0044; KEGG: mms:mma_2239 hypothetical protein. (163 aa)
derRibosome-associated GTPase EngA; GTPase that plays an essential role in the late steps of ribosome biogenesis; Belongs to the TRAFAC class TrmE-Era-EngA-EngB-Septin-like GTPase superfamily. EngA (Der) GTPase family. (457 aa)
rlmNRadical SAM enzyme, Cfr family; Specifically methylates position 2 of adenine 2503 in 23S rRNA and position 2 of adenine 37 in tRNAs. m2A2503 modification seems to play a crucial role in the proofreading step occurring at the peptidyl transferase center and thus would serve to optimize ribosomal fidelity; Belongs to the radical SAM superfamily. RlmN family. (379 aa)
Tint_1779RNA-binding S4 domain protein; KEGG: vap:Vapar_2182 pseudouridine synthase; PFAM: RNA-binding S4 domain protein; pseudouridine synthase; SMART: RNA-binding S4 domain protein; Belongs to the pseudouridine synthase RsuA family. (562 aa)
rlmBRNA methyltransferase, TrmH family, group 3; Specifically methylates the ribose of guanosine 2251 in 23S rRNA. (242 aa)
Tint_2189PFAM: pseudouridine synthase; RNA-binding S4 domain protein; KEGG: pol:Bpro_0606 ribosomal large subunit pseudouridine synthase F. (300 aa)
rsfSIojap-like protein; Functions as a ribosomal silencing factor. Interacts with ribosomal protein L14 (rplN), blocking formation of intersubunit bridge B8. Prevents association of the 30S and 50S ribosomal subunits and the formation of functional ribosomes, thus repressing translation. (257 aa)
rlmHProtein of unknown function DUF163; Specifically methylates the pseudouridine at position 1915 (m3Psi1915) in 23S rRNA; Belongs to the RNA methyltransferase RlmH family. (156 aa)
eraGTP-binding protein 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. (301 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. (276 aa)
Tint_2395PFAM: protein of unknown function DUF177; KEGG: lch:Lcho_0614 hypothetical protein. (180 aa)
Tint_2405Pseudouridine synthase, RluA family; Responsible for synthesis of pseudouridine from uracil. Belongs to the pseudouridine synthase RluA family. (329 aa)
rneRibonuclease, Rne/Rng family; Endoribonuclease that plays a central role in RNA processing and decay. Required for the maturation of 5S and 16S rRNAs and the majority of tRNAs. Also involved in the degradation of most mRNAs. Belongs to the RNase E/G family. RNase E subfamily. (998 aa)
Tint_2546Holliday junction resolvase YqgF; Could be a nuclease involved in processing of the 5'-end of pre-16S rRNA; Belongs to the YqgF HJR family. (137 aa)
Tint_2666PFAM: domain of unknown function DUF1732; YicC domain protein; KEGG: ctt:CtCNB1_3789 hypothetical protein. (292 aa)
rphRibonuclease PH; Phosphorolytic 3'-5' exoribonuclease that plays an important role in tRNA 3'-end maturation. Removes nucleotide residues following the 3'-CCA terminus of tRNAs; can also add nucleotides to the ends of RNA molecules by using nucleoside diphosphates as substrates, but this may not be physiologically important. Probably plays a role in initiation of 16S rRNA degradation (leading to ribosome degradation) during starvation. (243 aa)
ybeYProtein of unknown function UPF0054; Single strand-specific metallo-endoribonuclease involved in late-stage 70S ribosome quality control and in maturation of the 3' terminus of the 16S rRNA. (175 aa)
Tint_2901Sun protein; Specifically methylates the cytosine at position 967 (m5C967) of 16S rRNA. (457 aa)
rsmGMethyltransferase GidB; Specifically methylates the N7 position of guanine in position 527 of 16S rRNA. (224 aa)
Your Current Organism:
Thiomonas intermedia
NCBI taxonomy Id: 75379
Other names: T. intermedia K12, Thiobacillus intermedius K12, Thiomonas intermedia K12, Thiomonas intermedia str. K12, Thiomonas intermedia strain K12
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