(28 nodes) Single-species biofilm formation network (Pseudomonas agarici)

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:
	AWM79_18575	Pyocin activator protein PrtN; Incomplete; partial in the middle of a contig; missing stop; Derived by automated computational analysis using gene prediction method: Protein Homology. (82 aa)
	AMB87308.1	Diguanylate cyclase response regulator; Derived by automated computational analysis using gene prediction method: Protein Homology. (561 aa)
	lon-2	DNA-binding protein; ATP-dependent serine protease that mediates the selective degradation of mutant and abnormal proteins as well as certain short- lived regulatory proteins. Required for cellular homeostasis and for survival from DNA damage and developmental changes induced by stress. Degrades polypeptides processively to yield small peptide fragments that are 5 to 10 amino acids long. Binds to DNA in a double-stranded, site-specific manner. (798 aa)
	rhlE	DEAD/DEAH box helicase; DEAD-box RNA helicase involved in ribosome assembly. Has RNA- dependent ATPase activity and unwinds double-stranded RNA. (619 aa)
	AMB86945.1	GTP-binding protein; Derived by automated computational analysis using gene prediction method: Protein Homology. (213 aa)
	AMB84177.1	Exopolyphosphatase; Derived by automated computational analysis using gene prediction method: Protein Homology; Belongs to the GppA/Ppx family. (500 aa)
	AMB84220.1	Fimbrial protein; Derived by automated computational analysis using gene prediction method: Protein Homology. (187 aa)
	AMB84228.1	Hypothetical protein; Derived by automated computational analysis using gene prediction method: Protein Homology. (117 aa)
	AMB84258.1	Histidine kinase; Derived by automated computational analysis using gene prediction method: Protein Homology. (466 aa)
	AMB85018.1	Sugar transporter; Derived by automated computational analysis using gene prediction method: Protein Homology. (456 aa)
	AMB85017.1	Transporter; Derived by automated computational analysis using gene prediction method: Protein Homology. (329 aa)
	AMB85016.1	Glycosyl transferase family 1; Derived by automated computational analysis using gene prediction method: Protein Homology. (510 aa)
	AMB86071.1	Response regulator SirA; Derived by automated computational analysis using gene prediction method: Protein Homology; Belongs to the sulfur carrier protein TusA family. (79 aa)
	AWM79_06705	ABC transporter substrate-binding protein; Internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology. (456 aa)
	purN	Phosphoribosylglycinamide formyltransferase; Catalyzes the transfer of a formyl group from 10- formyltetrahydrofolate to 5-phospho-ribosyl-glycinamide (GAR), producing 5-phospho-ribosyl-N-formylglycinamide (FGAR) and tetrahydrofolate. (220 aa)
	AMB84583.1	Diguanylate cyclase; Derived by automated computational analysis using gene prediction method: Protein Homology. (683 aa)
	AMB84992.1	Glycosyltransferase; Derived by automated computational analysis using gene prediction method: Protein Homology. (435 aa)
	AMB85019.1	Penicillin-binding protein activator LpoB; Derived by automated computational analysis using gene prediction method: Protein Homology. (173 aa)
	AMB85020.1	Biofilm formation protein PelB; Derived by automated computational analysis using gene prediction method: Protein Homology. (1196 aa)
	AMB85021.1	PbsX family transcriptional regulator; Derived by automated computational analysis using gene prediction method: Protein Homology. (939 aa)
	AMB85027.1	Autotransporter outer membrane beta-barrel domain-containing protein; Derived by automated computational analysis using gene prediction method: Protein Homology. (640 aa)
	AMB87843.1	Universal stress protein UspA; Derived by automated computational analysis using gene prediction method: Protein Homology. (286 aa)
	AMB85815.1	Hypothetical protein; Derived by automated computational analysis using gene prediction method: Protein Homology. (223 aa)
	AMB86182.1	Hypothetical protein; Derived by automated computational analysis using gene prediction method: Protein Homology. (689 aa)
	AMB86769.1	Pilus assembly protein TapA; Derived by automated computational analysis using gene prediction method: Protein Homology; Belongs to the N-Me-Phe pilin family. (143 aa)
	AMB86541.1	GTP-binding protein TypA; Derived by automated computational analysis using gene prediction method: Protein Homology. (606 aa)
	AMB86362.1	Phosphate-binding protein; Derived by automated computational analysis using gene prediction method: Protein Homology. (332 aa)
	AMB87134.1	Pseudouridine synthase; Derived by automated computational analysis using gene prediction method: Protein Homology. (109 aa)

Your Current Organism:

Pseudomonas agarici

NCBI taxonomy Id: 46677
Other names: ATCC 25941, CCUG 32769, CFBP 2063, CIP 106703, DSM 11810, ICMP 2656, JCM 12566, LMG 2112, LMG:2112, NCPPB 2289, P. agarici

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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
AMB84258.1	AMB86182.1	AWM79_02640	AWM79_13085	Histidine kinase; Derived by automated computational analysis using gene prediction method: Protein Homology.	Hypothetical protein; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.411
AMB84583.1	AMB86182.1	AWM79_04345	AWM79_13085	Diguanylate cyclase; Derived by automated computational analysis using gene prediction method: Protein Homology.	Hypothetical protein; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.478
AMB85016.1	AMB85017.1	AWM79_06710	AWM79_06715	Glycosyl transferase family 1; Derived by automated computational analysis using gene prediction method: Protein Homology.	Transporter; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.966
AMB85016.1	AMB85018.1	AWM79_06710	AWM79_06720	Glycosyl transferase family 1; Derived by automated computational analysis using gene prediction method: Protein Homology.	Sugar transporter; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.968
AMB85016.1	AMB85019.1	AWM79_06710	AWM79_06725	Glycosyl transferase family 1; Derived by automated computational analysis using gene prediction method: Protein Homology.	Penicillin-binding protein activator LpoB; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.961
AMB85016.1	AMB85020.1	AWM79_06710	AWM79_06730	Glycosyl transferase family 1; Derived by automated computational analysis using gene prediction method: Protein Homology.	Biofilm formation protein PelB; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.942
AMB85016.1	AMB85021.1	AWM79_06710	AWM79_06735	Glycosyl transferase family 1; Derived by automated computational analysis using gene prediction method: Protein Homology.	PbsX family transcriptional regulator; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.949
AMB85016.1	AWM79_06705	AWM79_06710	AWM79_06705	Glycosyl transferase family 1; Derived by automated computational analysis using gene prediction method: Protein Homology.	ABC transporter substrate-binding protein; Internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.963
AMB85017.1	AMB85016.1	AWM79_06715	AWM79_06710	Transporter; Derived by automated computational analysis using gene prediction method: Protein Homology.	Glycosyl transferase family 1; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.966
AMB85017.1	AMB85018.1	AWM79_06715	AWM79_06720	Transporter; Derived by automated computational analysis using gene prediction method: Protein Homology.	Sugar transporter; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.967
AMB85017.1	AMB85019.1	AWM79_06715	AWM79_06725	Transporter; Derived by automated computational analysis using gene prediction method: Protein Homology.	Penicillin-binding protein activator LpoB; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.975
AMB85017.1	AMB85020.1	AWM79_06715	AWM79_06730	Transporter; Derived by automated computational analysis using gene prediction method: Protein Homology.	Biofilm formation protein PelB; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.945
AMB85017.1	AMB85021.1	AWM79_06715	AWM79_06735	Transporter; Derived by automated computational analysis using gene prediction method: Protein Homology.	PbsX family transcriptional regulator; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.946
AMB85017.1	AWM79_06705	AWM79_06715	AWM79_06705	Transporter; Derived by automated computational analysis using gene prediction method: Protein Homology.	ABC transporter substrate-binding protein; Internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.963
AMB85018.1	AMB85016.1	AWM79_06720	AWM79_06710	Sugar transporter; Derived by automated computational analysis using gene prediction method: Protein Homology.	Glycosyl transferase family 1; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.968
AMB85018.1	AMB85017.1	AWM79_06720	AWM79_06715	Sugar transporter; Derived by automated computational analysis using gene prediction method: Protein Homology.	Transporter; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.967
AMB85018.1	AMB85019.1	AWM79_06720	AWM79_06725	Sugar transporter; Derived by automated computational analysis using gene prediction method: Protein Homology.	Penicillin-binding protein activator LpoB; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.982
AMB85018.1	AMB85020.1	AWM79_06720	AWM79_06730	Sugar transporter; Derived by automated computational analysis using gene prediction method: Protein Homology.	Biofilm formation protein PelB; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.943
AMB85018.1	AMB85021.1	AWM79_06720	AWM79_06735	Sugar transporter; Derived by automated computational analysis using gene prediction method: Protein Homology.	PbsX family transcriptional regulator; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.949
AMB85018.1	AWM79_06705	AWM79_06720	AWM79_06705	Sugar transporter; Derived by automated computational analysis using gene prediction method: Protein Homology.	ABC transporter substrate-binding protein; Internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.	0.963