(32 nodes) Innate Immune System network (Geosporobacter ferrireducens)

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:
	AOT72269.1	Phage tail protein; Derived by automated computational analysis using gene prediction method: Protein Homology. (200 aa)
	deoC	Deoxyribose-phosphate aldolase; Catalyzes a reversible aldol reaction between acetaldehyde and D-glyceraldehyde 3-phosphate to generate 2-deoxy-D-ribose 5- phosphate; Belongs to the DeoC/FbaB aldolase family. DeoC type 1 subfamily. (222 aa)
	AOT72955.1	Cytidine deaminase; This enzyme scavenges exogenous and endogenous cytidine and 2'-deoxycytidine for UMP synthesis; Belongs to the cytidine and deoxycytidylate deaminase family. (125 aa)
	AOT68883.1	Hypothetical protein; Derived by automated computational analysis using gene prediction method: GeneMarkS+. (65 aa)
	AOT68962.1	Hypothetical protein; Derived by automated computational analysis using gene prediction method: Protein Homology. (238 aa)
	AOT69049.1	Hypothetical protein; Derived by automated computational analysis using gene prediction method: Protein Homology. (305 aa)
	AOT69681.1	Hypothetical protein; Derived by automated computational analysis using gene prediction method: Protein Homology. (213 aa)
	AOT69694.1	Hypothetical protein; Derived by automated computational analysis using gene prediction method: Protein Homology. (376 aa)
	AOT72396.1	Delta-aminolevulinic acid dehydratase; Derived by automated computational analysis using gene prediction method: Protein Homology; Belongs to the ALAD family. (326 aa)
	AOT69732.1	Hypothetical protein; Derived by automated computational analysis using gene prediction method: GeneMarkS+. (246 aa)
	AOT69784.1	Hypothetical protein; Derived by automated computational analysis using gene prediction method: Protein Homology. (429 aa)
	AOT69976.1	Hypothetical protein; Derived by automated computational analysis using gene prediction method: GeneMarkS+. (582 aa)
	AOT73075.1	Flagellin; Flagellin is the subunit protein which polymerizes to form the filaments of bacterial flagella. (271 aa)
	AOT70028.1	Hypothetical protein; Derived by automated computational analysis using gene prediction method: GeneMarkS+; Belongs to the bacterial flagellin family. (555 aa)
	atpD-2	ATPase; Produces ATP from ADP in the presence of a proton gradient across the membrane. (207 aa)
	atpB-2	V-type ATP synthase subunit B; Produces ATP from ADP in the presence of a proton gradient across the membrane. The V-type beta chain is a regulatory subunit. (457 aa)
	atpA-2	V-type ATP synthase subunit A; Produces ATP from ADP in the presence of a proton gradient across the membrane. The V-type alpha chain is a catalytic subunit. Belongs to the ATPase alpha/beta chains family. (589 aa)
	AOT70111.1	Hypothetical protein; Derived by automated computational analysis using gene prediction method: GeneMarkS+. (213 aa)
	AOT70112.1	ATP synthase subunit F; Derived by automated computational analysis using gene prediction method: Protein Homology. (102 aa)
	AOT70114.1	Hypothetical protein; Derived by automated computational analysis using gene prediction method: Protein Homology; Belongs to the V-ATPase 116 kDa subunit family. (655 aa)
	AOT70115.1	Hypothetical protein; Derived by automated computational analysis using gene prediction method: Protein Homology. (348 aa)
	AOT72729.1	Nicotinate phosphoribosyltransferase; Derived by automated computational analysis using gene prediction method: Protein Homology. (344 aa)
	AOT70165.1	D-lysine 5,6-aminomutase subunit alpha; Derived by automated computational analysis using gene prediction method: Protein Homology. (518 aa)
	AOT70370.1	Hypothetical protein; Derived by automated computational analysis using gene prediction method: GeneMarkS+. (246 aa)
	serS	serine--tRNA ligase; Catalyzes the attachment of serine to tRNA(Ser). Is also able to aminoacylate tRNA(Sec) with serine, to form the misacylated tRNA L- seryl-tRNA(Sec), which will be further converted into selenocysteinyl- tRNA(Sec). (425 aa)
	AOT70840.1	PEP phosphonomutase; Derived by automated computational analysis using gene prediction method: Protein Homology. (303 aa)
	xpt	Xanthine phosphoribosyltransferase; Converts the preformed base xanthine, a product of nucleic acid breakdown, to xanthosine 5'-monophosphate (XMP), so it can be reused for RNA or DNA synthesis. (190 aa)
	AOT71054.1	Pur operon repressor; Derived by automated computational analysis using gene prediction method: Protein Homology. (271 aa)
	sbcD	Exonuclease sbcCD subunit D; SbcCD cleaves DNA hairpin structures. These structures can inhibit DNA replication and are intermediates in certain DNA recombination reactions. The complex acts as a 3'->5' double strand exonuclease that can open hairpins. It also has a 5' single-strand endonuclease activity; Belongs to the SbcD family. (382 aa)
	apt	Adenine phosphoribosyltransferase; Catalyzes a salvage reaction resulting in the formation of AMP, that is energically less costly than de novo synthesis. (170 aa)
	AOT71939.1	Flagellin; Flagellin is the subunit protein which polymerizes to form the filaments of bacterial flagella. (273 aa)
	pgi	Glucose-6-phosphate isomerase; Derived by automated computational analysis using gene prediction method: Protein Homology; Belongs to the GPI family. (447 aa)

Your Current Organism:

Geosporobacter ferrireducens

NCBI taxonomy Id: 1424294
Other names: G. ferrireducens, Geosporobacter sp. IRF9, JCM 19987, KCTC 15395, strain IRF9

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
AOT68883.1	AOT72955.1	Gferi_04520	Gferi_02245	Hypothetical protein; Derived by automated computational analysis using gene prediction method: GeneMarkS+.	Cytidine deaminase; This enzyme scavenges exogenous and endogenous cytidine and 2'-deoxycytidine for UMP synthesis; Belongs to the cytidine and deoxycytidylate deaminase family.	0.414
AOT69732.1	AOT69976.1	Gferi_09135	Gferi_10495	Hypothetical protein; Derived by automated computational analysis using gene prediction method: GeneMarkS+.	Hypothetical protein; Derived by automated computational analysis using gene prediction method: GeneMarkS+.	0.423
AOT69976.1	AOT69732.1	Gferi_10495	Gferi_09135	Hypothetical protein; Derived by automated computational analysis using gene prediction method: GeneMarkS+.	Hypothetical protein; Derived by automated computational analysis using gene prediction method: GeneMarkS+.	0.423
AOT70028.1	AOT71939.1	Gferi_10775	Gferi_21800	Hypothetical protein; Derived by automated computational analysis using gene prediction method: GeneMarkS+; Belongs to the bacterial flagellin family.	Flagellin; Flagellin is the subunit protein which polymerizes to form the filaments of bacterial flagella.	0.737
AOT70028.1	AOT73075.1	Gferi_10775	Gferi_10755	Hypothetical protein; Derived by automated computational analysis using gene prediction method: GeneMarkS+; Belongs to the bacterial flagellin family.	Flagellin; Flagellin is the subunit protein which polymerizes to form the filaments of bacterial flagella.	0.818
AOT70111.1	AOT70112.1	Gferi_11225	Gferi_11230	Hypothetical protein; Derived by automated computational analysis using gene prediction method: GeneMarkS+.	ATP synthase subunit F; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.999
AOT70111.1	AOT70114.1	Gferi_11225	Gferi_11240	Hypothetical protein; Derived by automated computational analysis using gene prediction method: GeneMarkS+.	Hypothetical protein; Derived by automated computational analysis using gene prediction method: Protein Homology; Belongs to the V-ATPase 116 kDa subunit family.	0.998
AOT70111.1	AOT70115.1	Gferi_11225	Gferi_11245	Hypothetical protein; Derived by automated computational analysis using gene prediction method: GeneMarkS+.	Hypothetical protein; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.999
AOT70111.1	atpA-2	Gferi_11225	Gferi_11220	Hypothetical protein; Derived by automated computational analysis using gene prediction method: GeneMarkS+.	V-type ATP synthase subunit A; Produces ATP from ADP in the presence of a proton gradient across the membrane. The V-type alpha chain is a catalytic subunit. Belongs to the ATPase alpha/beta chains family.	0.999
AOT70111.1	atpB-2	Gferi_11225	Gferi_11215	Hypothetical protein; Derived by automated computational analysis using gene prediction method: GeneMarkS+.	V-type ATP synthase subunit B; Produces ATP from ADP in the presence of a proton gradient across the membrane. The V-type beta chain is a regulatory subunit.	0.999
AOT70111.1	atpD-2	Gferi_11225	Gferi_11210	Hypothetical protein; Derived by automated computational analysis using gene prediction method: GeneMarkS+.	ATPase; Produces ATP from ADP in the presence of a proton gradient across the membrane.	0.998
AOT70112.1	AOT70111.1	Gferi_11230	Gferi_11225	ATP synthase subunit F; Derived by automated computational analysis using gene prediction method: Protein Homology.	Hypothetical protein; Derived by automated computational analysis using gene prediction method: GeneMarkS+.	0.999
AOT70112.1	AOT70114.1	Gferi_11230	Gferi_11240	ATP synthase subunit F; Derived by automated computational analysis using gene prediction method: Protein Homology.	Hypothetical protein; Derived by automated computational analysis using gene prediction method: Protein Homology; Belongs to the V-ATPase 116 kDa subunit family.	0.999
AOT70112.1	AOT70115.1	Gferi_11230	Gferi_11245	ATP synthase subunit F; Derived by automated computational analysis using gene prediction method: Protein Homology.	Hypothetical protein; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.999
AOT70112.1	atpA-2	Gferi_11230	Gferi_11220	ATP synthase subunit F; Derived by automated computational analysis using gene prediction method: Protein Homology.	V-type ATP synthase subunit A; Produces ATP from ADP in the presence of a proton gradient across the membrane. The V-type alpha chain is a catalytic subunit. Belongs to the ATPase alpha/beta chains family.	0.999
AOT70112.1	atpB-2	Gferi_11230	Gferi_11215	ATP synthase subunit F; Derived by automated computational analysis using gene prediction method: Protein Homology.	V-type ATP synthase subunit B; Produces ATP from ADP in the presence of a proton gradient across the membrane. The V-type beta chain is a regulatory subunit.	0.999
AOT70112.1	atpD-2	Gferi_11230	Gferi_11210	ATP synthase subunit F; Derived by automated computational analysis using gene prediction method: Protein Homology.	ATPase; Produces ATP from ADP in the presence of a proton gradient across the membrane.	0.999
AOT70114.1	AOT70111.1	Gferi_11240	Gferi_11225	Hypothetical protein; Derived by automated computational analysis using gene prediction method: Protein Homology; Belongs to the V-ATPase 116 kDa subunit family.	Hypothetical protein; Derived by automated computational analysis using gene prediction method: GeneMarkS+.	0.998
AOT70114.1	AOT70112.1	Gferi_11240	Gferi_11230	Hypothetical protein; Derived by automated computational analysis using gene prediction method: Protein Homology; Belongs to the V-ATPase 116 kDa subunit family.	ATP synthase subunit F; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.999
AOT70114.1	AOT70115.1	Gferi_11240	Gferi_11245	Hypothetical protein; Derived by automated computational analysis using gene prediction method: Protein Homology; Belongs to the V-ATPase 116 kDa subunit family.	Hypothetical protein; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.999