(27 nodes) Mixed, incl. tRNA processing, and tRNA threonylcarbamoyladenosine modification network (Parabacteroides merdae)

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.

Node Color

colored nodes:
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:
	yeaZ	UGMP family protein. (239 aa)
	gcp	t(6)A37 threonylcarbamoyladenosine biosynthesis protein; Required for the formation of a threonylcarbamoyl group on adenosine at position 37 (t(6)A37) in tRNAs that read codons beginning with adenine. Is involved in the transfer of the threonylcarbamoyl moiety of threonylcarbamoyl-AMP (TC-AMP) to the N6 group of A37, together with TsaE and TsaB. TsaD likely plays a direct catalytic role in this reaction; Belongs to the KAE1 / TsaD family. (342 aa)
	yjbR	Uncharacterized protein conserved in bacteria. (118 aa)
	CUO81027.1	Uncharacterised protein family UPF0102; Belongs to the UPF0102 family. (128 aa)
	CUO81066.1	Uncharacterised protein. (75 aa)
	tadA_1	tRNA-specific adenosine deaminase; Catalyzes the deamination of adenosine to inosine at the wobble position 34 of tRNA(Arg2); Belongs to the cytidine and deoxycytidylate deaminase family. (147 aa)
	yciO	Putative translation factor (SUA5); Belongs to the SUA5 family. (202 aa)
	dgt	Deoxyguanosinetriphosphate triphosphohydrolase. (441 aa)
	dus_1	Probable tRNA-dihydrouridine synthase; Catalyzes the synthesis of 5,6-dihydrouridine (D), a modified base found in the D-loop of most tRNAs, via the reduction of the C5-C6 double bond in target uridines; Belongs to the dus family. (343 aa)
	ydiB	ADP-binding protein. (139 aa)
	CUO89183.1	Uncharacterised protein. (71 aa)
	minD	Cell division inhibitor MinD; Binds and transfers iron-sulfur (Fe-S) clusters to target apoproteins. Can hydrolyze ATP; Belongs to the Mrp/NBP35 ATP-binding proteins family. (369 aa)
	trmB	tRNA (guanine-N(7)-)-methyltransferase; Catalyzes the formation of N(7)-methylguanine at position 46 (m7G46) in tRNA. (252 aa)
	prmA	Ribosomal protein L11 methyltransferase; Methylates ribosomal protein L11; Belongs to the methyltransferase superfamily. PrmA family. (283 aa)
	CUP16044.1	Gas vesicle protein. (73 aa)
	CUP16077.1	Protein of uncharacterised function (DUF1469). (136 aa)
	CUP16111.1	Uncharacterised protein. (125 aa)
	miaA_1	tRNA dimethylallyltransferase; Catalyzes the transfer of a dimethylallyl group onto the adenine at position 37 in tRNAs that read codons beginning with uridine, leading to the formation of N6-(dimethylallyl)adenosine (i(6)A); Belongs to the IPP transferase family. (305 aa)
	miaA_2	tRNA dimethylallyltransferase; Catalyzes the transfer of a dimethylallyl group onto the adenine at position 37 in tRNAs that read codons beginning with uridine, leading to the formation of N6-(dimethylallyl)adenosine (i(6)A); Belongs to the IPP transferase family. (302 aa)
	rlmN	Ribosomal RNA large subunit methyltransferase N; Specifically methylates position 2 of adenine 2503 in 23S rRNA and position 2 of adenine 37 in tRNAs; Belongs to the radical SAM superfamily. RlmN family. (343 aa)
	rsmF	Ribosomal RNA small subunit methyltransferase F. (465 aa)
	miaB_2	(Dimethylallyl)adenosine tRNA methylthiotransferase MiaB; Catalyzes the methylthiolation of N6-(dimethylallyl)adenosine (i(6)A), leading to the formation of 2-methylthio-N6- (dimethylallyl)adenosine (ms(2)i(6)A) at position 37 in tRNAs that read codons beginning with uridine. (456 aa)
	CUP64748.1	Uncharacterised protein. (31 aa)
	CUP64802.1	Uncharacterised protein. (142 aa)
	tilS	tRNA(Ile)-lysidine synthase; Ligates lysine onto the cytidine present at position 34 of the AUA codon-specific tRNA(Ile) that contains the anticodon CAU, in an ATP-dependent manner. Cytidine is converted to lysidine, thus changing the amino acid specificity of the tRNA from methionine to isoleucine. Belongs to the tRNA(Ile)-lysidine synthase family. (444 aa)
	CUP72571.1	Chromosome segregation protein SMC. (254 aa)
	CUP72607.1	Metal-binding protein; Belongs to the GTP cyclohydrolase I type 2/NIF3 family. (365 aa)

Your Current Organism:

Parabacteroides merdae

NCBI taxonomy Id: 46503
Other names: ATCC 43184, Bacteroides merdae, CCUG 38734, CIP 104202, JCM 9497, NCTC 13052, P. merdae, VPI T4-1

Send network to Cytoscape

Export your current network:

... as a bitmap image:

download

file format is 'PNG': portable network graphic

... as a high-resolution bitmap:

download

same PNG format, but at higher resolution

... as a vector graphic:

download

SVG: scalable vector graphic - can be opened and edited in Illustrator, CorelDraw, Dia, etc

... as short tabular text output:

download

TSV: tab separated values - can be opened in Excel and Cytoscape (lists only one-way edges: A-B)

... as tabular text output:

download

TSV: tab separated values - can be opened in Excel (lists reciprocal edges: A-B,B-A)

... as an XML summary:

download

structured XML interaction data, according to the 'PSI-MI' data standard

... protein node degrees:

download

node degree of proteins in your network (given the current score cut-off)

... network coordinates:

download

a flat-file format describing the coordinates and colors of nodes in the network

... protein sequences:

download

MFA: multi-fasta format - containing the aminoacid sequences in the network

... protein annotations:

download

a tab-delimited file describing the names, domains and descriptions of proteins in your network

... functional annotations:

download

a tab-delimited file containing all known functional terms of proteins in your network

Browse interactions in tabular form:

node1	node2	node1 accession	node2 accession	node1 annotation	node2 annotation	score
CUO81027.1	CUO81066.1	ERS852463_01110	ERS852463_01111	Uncharacterised protein family UPF0102; Belongs to the UPF0102 family.	Uncharacterised protein.	0.599
CUO81027.1	tadA_1	ERS852463_01110	ERS852463_01112	Uncharacterised protein family UPF0102; Belongs to the UPF0102 family.	tRNA-specific adenosine deaminase; Catalyzes the deamination of adenosine to inosine at the wobble position 34 of tRNA(Arg2); Belongs to the cytidine and deoxycytidylate deaminase family.	0.595
CUO81027.1	yjbR	ERS852463_01110	ERS852463_01109	Uncharacterised protein family UPF0102; Belongs to the UPF0102 family.	Uncharacterized protein conserved in bacteria.	0.798
CUO81066.1	CUO81027.1	ERS852463_01111	ERS852463_01110	Uncharacterised protein.	Uncharacterised protein family UPF0102; Belongs to the UPF0102 family.	0.599
CUO81066.1	tadA_1	ERS852463_01111	ERS852463_01112	Uncharacterised protein.	tRNA-specific adenosine deaminase; Catalyzes the deamination of adenosine to inosine at the wobble position 34 of tRNA(Arg2); Belongs to the cytidine and deoxycytidylate deaminase family.	0.791
CUO81066.1	yjbR	ERS852463_01111	ERS852463_01109	Uncharacterised protein.	Uncharacterized protein conserved in bacteria.	0.563
CUO89183.1	ydiB	ERS852463_01326	ERS852463_01325	Uncharacterised protein.	ADP-binding protein.	0.779
CUP16044.1	CUP16077.1	ERS852463_01949	ERS852463_01950	Gas vesicle protein.	Protein of uncharacterised function (DUF1469).	0.783
CUP16044.1	CUP16111.1	ERS852463_01949	ERS852463_01951	Gas vesicle protein.	Uncharacterised protein.	0.784
CUP16044.1	prmA	ERS852463_01949	ERS852463_01948	Gas vesicle protein.	Ribosomal protein L11 methyltransferase; Methylates ribosomal protein L11; Belongs to the methyltransferase superfamily. PrmA family.	0.538
CUP16077.1	CUP16044.1	ERS852463_01950	ERS852463_01949	Protein of uncharacterised function (DUF1469).	Gas vesicle protein.	0.783
CUP16077.1	CUP16111.1	ERS852463_01950	ERS852463_01951	Protein of uncharacterised function (DUF1469).	Uncharacterised protein.	0.784
CUP16077.1	prmA	ERS852463_01950	ERS852463_01948	Protein of uncharacterised function (DUF1469).	Ribosomal protein L11 methyltransferase; Methylates ribosomal protein L11; Belongs to the methyltransferase superfamily. PrmA family.	0.538
CUP16111.1	CUP16044.1	ERS852463_01951	ERS852463_01949	Uncharacterised protein.	Gas vesicle protein.	0.784
CUP16111.1	CUP16077.1	ERS852463_01951	ERS852463_01950	Uncharacterised protein.	Protein of uncharacterised function (DUF1469).	0.784
CUP16111.1	prmA	ERS852463_01951	ERS852463_01948	Uncharacterised protein.	Ribosomal protein L11 methyltransferase; Methylates ribosomal protein L11; Belongs to the methyltransferase superfamily. PrmA family.	0.538
CUP64748.1	CUP64802.1	ERS852463_03067	ERS852463_03068	Uncharacterised protein.	Uncharacterised protein.	0.530
CUP64748.1	miaB_2	ERS852463_03067	ERS852463_03066	Uncharacterised protein.	(Dimethylallyl)adenosine tRNA methylthiotransferase MiaB; Catalyzes the methylthiolation of N6-(dimethylallyl)adenosine (i(6)A), leading to the formation of 2-methylthio-N6- (dimethylallyl)adenosine (ms(2)i(6)A) at position 37 in tRNAs that read codons beginning with uridine.	0.727
CUP64802.1	CUP64748.1	ERS852463_03068	ERS852463_03067	Uncharacterised protein.	Uncharacterised protein.	0.530
CUP64802.1	miaB_2	ERS852463_03068	ERS852463_03066	Uncharacterised protein.	(Dimethylallyl)adenosine tRNA methylthiotransferase MiaB; Catalyzes the methylthiolation of N6-(dimethylallyl)adenosine (i(6)A), leading to the formation of 2-methylthio-N6- (dimethylallyl)adenosine (ms(2)i(6)A) at position 37 in tRNAs that read codons beginning with uridine.	0.501