tag protein (Desulfovibrio vulgaris Hildenborough)

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.

Knowledge-based Evidence

from curated databases

textmining

Assay-based Predictions

experimentally determined

co-expression

Genomic Predictions

gene neighborhood

gene co-occurrence

gene fusions

Your Current Organism:

Desulfovibrio vulgaris Hildenborough

NCBI taxonomy Id: 882
Other names: D. vulgaris str. Hildenborough, Desulfovibrio vulgaris (STRAIN HILDENBOROUGH), Desulfovibrio vulgaris ATCC 29579, Desulfovibrio vulgaris str. Hildenborough, Desulfovibrio vulgaris subsp. vulgaris (strain Hildenborough), Desulfovibrio vulgaris subsp. vulgaris ATCC 29579, Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough

Export your current network:

... as a bitmap image:

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file format is 'PNG': portable network graphic

... as a high-resolution bitmap:

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same PNG format, but at higher resolution

... as a vector graphic:

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

... as short tabular text output:

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

... as tabular text output:

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

... as an XML summary:

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

... protein node degrees:

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

... network coordinates:

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

... protein sequences:

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

... protein annotations:

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

... functional annotations:

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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
DVU_0355	DVU_0357	DVU_0355	DVU_0357	Sensory box/GGDEF domain protein; Identified by match to protein family HMM PF00785; match to protein family HMM PF00989; match to protein family HMM PF00990; match to protein family HMM TIGR00229; match to protein family HMM TIGR00254.	Conserved hypothetical protein; Identified by similarity to OMNI:NTL02ML5790.	0.549
DVU_0355	tag	DVU_0355	DVU_0356	Sensory box/GGDEF domain protein; Identified by match to protein family HMM PF00785; match to protein family HMM PF00989; match to protein family HMM PF00990; match to protein family HMM TIGR00229; match to protein family HMM TIGR00254.	DNA-3-methyladenine glycosylase I; Identified by similarity to SP:P05100; match to protein family HMM PF03352.	0.537
DVU_0357	DVU_0355	DVU_0357	DVU_0355	Conserved hypothetical protein; Identified by similarity to OMNI:NTL02ML5790.	Sensory box/GGDEF domain protein; Identified by match to protein family HMM PF00785; match to protein family HMM PF00989; match to protein family HMM PF00990; match to protein family HMM TIGR00229; match to protein family HMM TIGR00254.	0.549
DVU_0357	tag	DVU_0357	DVU_0356	Conserved hypothetical protein; Identified by similarity to OMNI:NTL02ML5790.	DNA-3-methyladenine glycosylase I; Identified by similarity to SP:P05100; match to protein family HMM PF03352.	0.761
DVU_1784	tag	DVU_1784	DVU_0356	Oxidoreductase, short-chain dehydrogenase/reductase family; Identified by match to protein family HMM PF00106; Belongs to the short-chain dehydrogenases/reductases (SDR) family.	DNA-3-methyladenine glycosylase I; Identified by similarity to SP:P05100; match to protein family HMM PF03352.	0.756
guaA	polA	DVU_1043	DVU_0496	GMP synthase; Catalyzes the synthesis of GMP from XMP.	DNA polymerase I; Identified by similarity to SP:P00582; match to protein family HMM PF00476; match to protein family HMM PF01367; match to protein family HMM PF02739; match to protein family HMM TIGR00593.	0.800
guaA	tag	DVU_1043	DVU_0356	GMP synthase; Catalyzes the synthesis of GMP from XMP.	DNA-3-methyladenine glycosylase I; Identified by similarity to SP:P05100; match to protein family HMM PF03352.	0.896
mutY	polA	DVU_0282	DVU_0496	A/G-specific adenine glycosylase; Identified by match to protein family HMM PF00293; match to protein family HMM PF00633; match to protein family HMM PF00730; match to protein family HMM TIGR01084.	DNA polymerase I; Identified by similarity to SP:P00582; match to protein family HMM PF00476; match to protein family HMM PF01367; match to protein family HMM PF02739; match to protein family HMM TIGR00593.	0.581
mutY	tag	DVU_0282	DVU_0356	A/G-specific adenine glycosylase; Identified by match to protein family HMM PF00293; match to protein family HMM PF00633; match to protein family HMM PF00730; match to protein family HMM TIGR01084.	DNA-3-methyladenine glycosylase I; Identified by similarity to SP:P05100; match to protein family HMM PF03352.	0.444
polA	guaA	DVU_0496	DVU_1043	DNA polymerase I; Identified by similarity to SP:P00582; match to protein family HMM PF00476; match to protein family HMM PF01367; match to protein family HMM PF02739; match to protein family HMM TIGR00593.	GMP synthase; Catalyzes the synthesis of GMP from XMP.	0.800
polA	mutY	DVU_0496	DVU_0282	DNA polymerase I; Identified by similarity to SP:P00582; match to protein family HMM PF00476; match to protein family HMM PF01367; match to protein family HMM PF02739; match to protein family HMM TIGR00593.	A/G-specific adenine glycosylase; Identified by match to protein family HMM PF00293; match to protein family HMM PF00633; match to protein family HMM PF00730; match to protein family HMM TIGR01084.	0.581
polA	tag	DVU_0496	DVU_0356	DNA polymerase I; Identified by similarity to SP:P00582; match to protein family HMM PF00476; match to protein family HMM PF01367; match to protein family HMM PF02739; match to protein family HMM TIGR00593.	DNA-3-methyladenine glycosylase I; Identified by similarity to SP:P05100; match to protein family HMM PF03352.	0.578
tag	DVU_0355	DVU_0356	DVU_0355	DNA-3-methyladenine glycosylase I; Identified by similarity to SP:P05100; match to protein family HMM PF03352.	Sensory box/GGDEF domain protein; Identified by match to protein family HMM PF00785; match to protein family HMM PF00989; match to protein family HMM PF00990; match to protein family HMM TIGR00229; match to protein family HMM TIGR00254.	0.537
tag	DVU_0357	DVU_0356	DVU_0357	DNA-3-methyladenine glycosylase I; Identified by similarity to SP:P05100; match to protein family HMM PF03352.	Conserved hypothetical protein; Identified by similarity to OMNI:NTL02ML5790.	0.761
tag	DVU_1784	DVU_0356	DVU_1784	DNA-3-methyladenine glycosylase I; Identified by similarity to SP:P05100; match to protein family HMM PF03352.	Oxidoreductase, short-chain dehydrogenase/reductase family; Identified by match to protein family HMM PF00106; Belongs to the short-chain dehydrogenases/reductases (SDR) family.	0.756
tag	guaA	DVU_0356	DVU_1043	DNA-3-methyladenine glycosylase I; Identified by similarity to SP:P05100; match to protein family HMM PF03352.	GMP synthase; Catalyzes the synthesis of GMP from XMP.	0.896
tag	mutY	DVU_0356	DVU_0282	DNA-3-methyladenine glycosylase I; Identified by similarity to SP:P05100; match to protein family HMM PF03352.	A/G-specific adenine glycosylase; Identified by match to protein family HMM PF00293; match to protein family HMM PF00633; match to protein family HMM PF00730; match to protein family HMM TIGR01084.	0.444
tag	polA	DVU_0356	DVU_0496	DNA-3-methyladenine glycosylase I; Identified by similarity to SP:P05100; match to protein family HMM PF03352.	DNA polymerase I; Identified by similarity to SP:P00582; match to protein family HMM PF00476; match to protein family HMM PF01367; match to protein family HMM PF02739; match to protein family HMM TIGR00593.	0.578

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