(32 nodes) RNA degradation network (Clostridium citroniae)

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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query proteins and first shell of interactors

white nodes:
second shell of interactors

Node Content

empty nodes:
proteins of unknown 3D structure

filled nodes:
a 3D structure is known or predicted

Edges:

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

Others

textmining

co-expression

protein homology

Your Input:
	SFR87936.1	ATP-dependent RNA helicase SUPV3L1/SUV3. (668 aa)
	rho	Transcription 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. (590 aa)
	SFR89011.1	GTPase, G3E family. (350 aa)
	rny	Ribonucrease Y; Endoribonuclease that initiates mRNA decay. Belongs to the RNase Y family. (516 aa)
	ppk	Polyphosphate kinase; Catalyzes the reversible transfer of the terminal phosphate of ATP to form a long-chain polyphosphate (polyP). Belongs to the polyphosphate kinase 1 (PPK1) family. (754 aa)
	SFS04797.1	AAA-like domain-containing protein. (818 aa)
	rnr	Ribonuclease R; 3'-5' exoribonuclease that releases 5'-nucleoside monophosphates and is involved in maturation of structured RNAs. (755 aa)
	eno	Enolase; Catalyzes the reversible conversion of 2-phosphoglycerate into phosphoenolpyruvate. It is essential for the degradation of carbohydrates via glycolysis; Belongs to the enolase family. (425 aa)
	SFR96351.1	Uncharacterized protein. (172 aa)
	recQ	ATP-dependent DNA helicase RecQ. (787 aa)
	SFS15178.1	ATP-dependent RNA helicase DeaD; Belongs to the DEAD box helicase family. (569 aa)
	SFS18142.1	GTPase, G3E family. (350 aa)
	SFS18990.1	DNA topoisomerase-3. (696 aa)
	SFS18189.1	Hypothetical protein. (329 aa)
	eno-2	Enolase; Catalyzes the reversible conversion of 2-phosphoglycerate into phosphoenolpyruvate. It is essential for the degradation of carbohydrates via glycolysis; Belongs to the enolase family. (431 aa)
	SFS20654.1	Ribonuclease G. (401 aa)
	pap	polyphosphate:AMP phosphotransferase. (501 aa)
	pnp	Polyribonucleotide nucleotidyltransferase; Involved in mRNA degradation. Catalyzes the phosphorolysis of single-stranded polyribonucleotides processively in the 3'- to 5'- direction. (706 aa)
	SFS22239.1	Uncharacterized conserved protein, LabA/DUF88 family. (312 aa)
	SFS23453.1	ATP-dependent RNA helicase DbpA. (486 aa)
	SFS23687.1	spoIIIJ-associated protein. (265 aa)
	SFS04952.1	tRNA nucleotidyltransferase (CCA-adding enzyme). (429 aa)
	SFS06968.1	comF family protein. (241 aa)
	SFS10193.1	HDIG domain-containing protein. (198 aa)
	groL	Chaperonin GroEL; Prevents misfolding and promotes the refolding and proper assembly of unfolded polypeptides generated under stress conditions. (540 aa)
	rnj	Ribonuclease J; An RNase that has 5'-3' exonuclease and possibly endonuclease activity. Involved in maturation of rRNA and in some organisms also mRNA maturation and/or decay. (748 aa)
	dnaK	Molecular chaperone DnaK; Acts as a chaperone; Belongs to the heat shock protein 70 family. (620 aa)
	SFS15778.1	tRNA nucleotidyltransferase (CCA-adding enzyme). (380 aa)
	pfkA	6-phosphofructokinase; Catalyzes the phosphorylation of D-fructose 6-phosphate to fructose 1,6-bisphosphate by ATP, the first committing step of glycolysis. (324 aa)
	SFS16881.1	DNA topoisomerase-3. (705 aa)
	SFS16938.1	2''-aminoglycoside nucleotidyltransferase. (172 aa)
	SFS15120.1	GTPase, G3E family. (371 aa)

Your Current Organism:

Clostridium citroniae

NCBI taxonomy Id: 358743
Other names: CCUG 52203, Clostridium citroniae Warren et al. 2007, DSM 19261, [. citroniae, [Clostridium] citroniae, strain RMA 16102

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Browse interactions in tabular form:

node1	node2	node1 accession	node2 accession	node1 annotation	node2 annotation	score
SFR87936.1	SFS15178.1	SAMN05216568_101387	SAMN05216568_10497	ATP-dependent RNA helicase SUPV3L1/SUV3.	ATP-dependent RNA helicase DeaD; Belongs to the DEAD box helicase family.	0.978
SFR87936.1	SFS23453.1	SAMN05216568_101387	SAMN05216568_11485	ATP-dependent RNA helicase SUPV3L1/SUV3.	ATP-dependent RNA helicase DbpA.	0.978
SFR87936.1	dnaK	SAMN05216568_101387	SAMN05216568_104109	ATP-dependent RNA helicase SUPV3L1/SUV3.	Molecular chaperone DnaK; Acts as a chaperone; Belongs to the heat shock protein 70 family.	0.461
SFR96351.1	SFS04952.1	SAMN05216568_1011275	SAMN05216568_102410	Uncharacterized protein.	tRNA nucleotidyltransferase (CCA-adding enzyme).	0.457
SFR96351.1	SFS15778.1	SAMN05216568_1011275	SAMN05216568_104206	Uncharacterized protein.	tRNA nucleotidyltransferase (CCA-adding enzyme).	0.457
SFR96351.1	pnp	SAMN05216568_1011275	SAMN05216568_1078	Uncharacterized protein.	Polyribonucleotide nucleotidyltransferase; Involved in mRNA degradation. Catalyzes the phosphorolysis of single-stranded polyribonucleotides processively in the 3'- to 5'- direction.	0.431
SFR96351.1	rny	SAMN05216568_1011275	SAMN05216568_101762	Uncharacterized protein.	Ribonucrease Y; Endoribonuclease that initiates mRNA decay. Belongs to the RNase Y family.	0.460
SFS04952.1	SFR96351.1	SAMN05216568_102410	SAMN05216568_1011275	tRNA nucleotidyltransferase (CCA-adding enzyme).	Uncharacterized protein.	0.457
SFS04952.1	eno	SAMN05216568_102410	SAMN05216568_1011288	tRNA nucleotidyltransferase (CCA-adding enzyme).	Enolase; Catalyzes the reversible conversion of 2-phosphoglycerate into phosphoenolpyruvate. It is essential for the degradation of carbohydrates via glycolysis; Belongs to the enolase family.	0.453
SFS04952.1	eno-2	SAMN05216568_102410	SAMN05216568_10587	tRNA nucleotidyltransferase (CCA-adding enzyme).	Enolase; Catalyzes the reversible conversion of 2-phosphoglycerate into phosphoenolpyruvate. It is essential for the degradation of carbohydrates via glycolysis; Belongs to the enolase family.	0.453
SFS04952.1	groL	SAMN05216568_102410	SAMN05216568_103138	tRNA nucleotidyltransferase (CCA-adding enzyme).	Chaperonin GroEL; Prevents misfolding and promotes the refolding and proper assembly of unfolded polypeptides generated under stress conditions.	0.453
SFS04952.1	pnp	SAMN05216568_102410	SAMN05216568_1078	tRNA nucleotidyltransferase (CCA-adding enzyme).	Polyribonucleotide nucleotidyltransferase; Involved in mRNA degradation. Catalyzes the phosphorolysis of single-stranded polyribonucleotides processively in the 3'- to 5'- direction.	0.720
SFS04952.1	rnr	SAMN05216568_102410	SAMN05216568_1011291	tRNA nucleotidyltransferase (CCA-adding enzyme).	Ribonuclease R; 3'-5' exoribonuclease that releases 5'-nucleoside monophosphates and is involved in maturation of structured RNAs.	0.486
SFS04952.1	rny	SAMN05216568_102410	SAMN05216568_101762	tRNA nucleotidyltransferase (CCA-adding enzyme).	Ribonucrease Y; Endoribonuclease that initiates mRNA decay. Belongs to the RNase Y family.	0.587
SFS06968.1	SFS15178.1	SAMN05216568_102606	SAMN05216568_10497	comF family protein.	ATP-dependent RNA helicase DeaD; Belongs to the DEAD box helicase family.	0.591
SFS06968.1	SFS23453.1	SAMN05216568_102606	SAMN05216568_11485	comF family protein.	ATP-dependent RNA helicase DbpA.	0.591
SFS10193.1	rny	SAMN05216568_103112	SAMN05216568_101762	HDIG domain-containing protein.	Ribonucrease Y; Endoribonuclease that initiates mRNA decay. Belongs to the RNase Y family.	0.437
SFS15178.1	SFR87936.1	SAMN05216568_10497	SAMN05216568_101387	ATP-dependent RNA helicase DeaD; Belongs to the DEAD box helicase family.	ATP-dependent RNA helicase SUPV3L1/SUV3.	0.978
SFS15178.1	SFS06968.1	SAMN05216568_10497	SAMN05216568_102606	ATP-dependent RNA helicase DeaD; Belongs to the DEAD box helicase family.	comF family protein.	0.591
SFS15178.1	SFS16881.1	SAMN05216568_10497	SAMN05216568_104399	ATP-dependent RNA helicase DeaD; Belongs to the DEAD box helicase family.	DNA topoisomerase-3.	0.408