dinB_2 protein (Clostridium chromiireducens)

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 Input:

Neighborhood

Gene Fusion

Cooccurrence

Coexpression

Experiments

Databases

Textmining

[Homology]

Score

dinB_2

DNA polymerase IV. (418 aa)

Predicted Functional Partners:

dnaN

0.888

recA

0.877

OPJ61151.1

0.870

lexA_2

0.847

lexA_3

0.816

lexA_1

0.815

nifJ_2

0.807

nifJ_3

0.807

nifJ_1

0.739

OPJ63500.1

0.726

Your Current Organism:

Clostridium chromiireducens

NCBI taxonomy Id: 225345
Other names: C. chromiireducens, Clostridium chromiireducens Inglett et al. 2011, DSM 23318, KCTC 5935, strain GCAF-1

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
OPJ61151.1	dinB_2	CLCHR_26560	CLCHR_26570	Hypothetical protein.	DNA polymerase IV.	0.870
OPJ63500.1	dinB_2	CLCHR_15980	CLCHR_26570	Hypothetical protein; 8-oxoguanine DNA glycosylase, N-terminal domain.	DNA polymerase IV.	0.726
OPJ63500.1	dnaN	CLCHR_15980	CLCHR_32490	Hypothetical protein; 8-oxoguanine DNA glycosylase, N-terminal domain.	DNA polymerase III subunit beta; Confers DNA tethering and processivity to DNA polymerases and other proteins. Acts as a clamp, forming a ring around DNA (a reaction catalyzed by the clamp-loading complex) which diffuses in an ATP- independent manner freely and bidirectionally along dsDNA. Initially characterized for its ability to contact the catalytic subunit of DNA polymerase III (Pol III), a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria; Pol III exhibits 3'-5' exonuclease proofreading activity. The beta chain is required for initiation of [...]	0.459
OPJ63500.1	recA	CLCHR_15980	CLCHR_06600	Hypothetical protein; 8-oxoguanine DNA glycosylase, N-terminal domain.	Protein RecA; Can catalyze the hydrolysis of ATP in the presence of single- stranded DNA, the ATP-dependent uptake of single-stranded DNA by duplex DNA, and the ATP-dependent hybridization of homologous single-stranded DNAs. It interacts with LexA causing its activation and leading to its autocatalytic cleavage; Belongs to the RecA family.	0.713
dinB_2	OPJ61151.1	CLCHR_26570	CLCHR_26560	DNA polymerase IV.	Hypothetical protein.	0.870
dinB_2	OPJ63500.1	CLCHR_26570	CLCHR_15980	DNA polymerase IV.	Hypothetical protein; 8-oxoguanine DNA glycosylase, N-terminal domain.	0.726
dinB_2	dnaN	CLCHR_26570	CLCHR_32490	DNA polymerase IV.	DNA polymerase III subunit beta; Confers DNA tethering and processivity to DNA polymerases and other proteins. Acts as a clamp, forming a ring around DNA (a reaction catalyzed by the clamp-loading complex) which diffuses in an ATP- independent manner freely and bidirectionally along dsDNA. Initially characterized for its ability to contact the catalytic subunit of DNA polymerase III (Pol III), a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria; Pol III exhibits 3'-5' exonuclease proofreading activity. The beta chain is required for initiation of [...]	0.888
dinB_2	lexA_1	CLCHR_26570	CLCHR_14770	DNA polymerase IV.	LexA repressor; Represses a number of genes involved in the response to DNA damage (SOS response), including recA and lexA. In the presence of single-stranded DNA, RecA interacts with LexA causing an autocatalytic cleavage which disrupts the DNA-binding part of LexA, leading to derepression of the SOS regulon and eventually DNA repair.	0.815
dinB_2	lexA_2	CLCHR_26570	CLCHR_45270	DNA polymerase IV.	LexA repressor; Represses a number of genes involved in the response to DNA damage (SOS response).	0.847
dinB_2	lexA_3	CLCHR_26570	CLCHR_45600	DNA polymerase IV.	LexA repressor; Represses a number of genes involved in the response to DNA damage (SOS response), including recA and lexA. In the presence of single-stranded DNA, RecA interacts with LexA causing an autocatalytic cleavage which disrupts the DNA-binding part of LexA, leading to derepression of the SOS regulon and eventually DNA repair.	0.816
dinB_2	nifJ_1	CLCHR_26570	CLCHR_02790	DNA polymerase IV.	Pyruvate-flavodoxin oxidoreductase.	0.739
dinB_2	nifJ_2	CLCHR_26570	CLCHR_11980	DNA polymerase IV.	Pyruvate-flavodoxin oxidoreductase.	0.807
dinB_2	nifJ_3	CLCHR_26570	CLCHR_46340	DNA polymerase IV.	Pyruvate-flavodoxin oxidoreductase.	0.807
dinB_2	recA	CLCHR_26570	CLCHR_06600	DNA polymerase IV.	Protein RecA; Can catalyze the hydrolysis of ATP in the presence of single- stranded DNA, the ATP-dependent uptake of single-stranded DNA by duplex DNA, and the ATP-dependent hybridization of homologous single-stranded DNAs. It interacts with LexA causing its activation and leading to its autocatalytic cleavage; Belongs to the RecA family.	0.877
dnaN	OPJ63500.1	CLCHR_32490	CLCHR_15980	DNA polymerase III subunit beta; Confers DNA tethering and processivity to DNA polymerases and other proteins. Acts as a clamp, forming a ring around DNA (a reaction catalyzed by the clamp-loading complex) which diffuses in an ATP- independent manner freely and bidirectionally along dsDNA. Initially characterized for its ability to contact the catalytic subunit of DNA polymerase III (Pol III), a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria; Pol III exhibits 3'-5' exonuclease proofreading activity. The beta chain is required for initiation of [...]	Hypothetical protein; 8-oxoguanine DNA glycosylase, N-terminal domain.	0.459
dnaN	dinB_2	CLCHR_32490	CLCHR_26570	DNA polymerase III subunit beta; Confers DNA tethering and processivity to DNA polymerases and other proteins. Acts as a clamp, forming a ring around DNA (a reaction catalyzed by the clamp-loading complex) which diffuses in an ATP- independent manner freely and bidirectionally along dsDNA. Initially characterized for its ability to contact the catalytic subunit of DNA polymerase III (Pol III), a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria; Pol III exhibits 3'-5' exonuclease proofreading activity. The beta chain is required for initiation of [...]	DNA polymerase IV.	0.888
dnaN	lexA_1	CLCHR_32490	CLCHR_14770	DNA polymerase III subunit beta; Confers DNA tethering and processivity to DNA polymerases and other proteins. Acts as a clamp, forming a ring around DNA (a reaction catalyzed by the clamp-loading complex) which diffuses in an ATP- independent manner freely and bidirectionally along dsDNA. Initially characterized for its ability to contact the catalytic subunit of DNA polymerase III (Pol III), a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria; Pol III exhibits 3'-5' exonuclease proofreading activity. The beta chain is required for initiation of [...]	LexA repressor; Represses a number of genes involved in the response to DNA damage (SOS response), including recA and lexA. In the presence of single-stranded DNA, RecA interacts with LexA causing an autocatalytic cleavage which disrupts the DNA-binding part of LexA, leading to derepression of the SOS regulon and eventually DNA repair.	0.483
dnaN	lexA_2	CLCHR_32490	CLCHR_45270	DNA polymerase III subunit beta; Confers DNA tethering and processivity to DNA polymerases and other proteins. Acts as a clamp, forming a ring around DNA (a reaction catalyzed by the clamp-loading complex) which diffuses in an ATP- independent manner freely and bidirectionally along dsDNA. Initially characterized for its ability to contact the catalytic subunit of DNA polymerase III (Pol III), a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria; Pol III exhibits 3'-5' exonuclease proofreading activity. The beta chain is required for initiation of [...]	LexA repressor; Represses a number of genes involved in the response to DNA damage (SOS response).	0.482
dnaN	lexA_3	CLCHR_32490	CLCHR_45600	DNA polymerase III subunit beta; Confers DNA tethering and processivity to DNA polymerases and other proteins. Acts as a clamp, forming a ring around DNA (a reaction catalyzed by the clamp-loading complex) which diffuses in an ATP- independent manner freely and bidirectionally along dsDNA. Initially characterized for its ability to contact the catalytic subunit of DNA polymerase III (Pol III), a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria; Pol III exhibits 3'-5' exonuclease proofreading activity. The beta chain is required for initiation of [...]	LexA repressor; Represses a number of genes involved in the response to DNA damage (SOS response), including recA and lexA. In the presence of single-stranded DNA, RecA interacts with LexA causing an autocatalytic cleavage which disrupts the DNA-binding part of LexA, leading to derepression of the SOS regulon and eventually DNA repair.	0.482
dnaN	recA	CLCHR_32490	CLCHR_06600	DNA polymerase III subunit beta; Confers DNA tethering and processivity to DNA polymerases and other proteins. Acts as a clamp, forming a ring around DNA (a reaction catalyzed by the clamp-loading complex) which diffuses in an ATP- independent manner freely and bidirectionally along dsDNA. Initially characterized for its ability to contact the catalytic subunit of DNA polymerase III (Pol III), a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria; Pol III exhibits 3'-5' exonuclease proofreading activity. The beta chain is required for initiation of [...]	Protein RecA; Can catalyze the hydrolysis of ATP in the presence of single- stranded DNA, the ATP-dependent uptake of single-stranded DNA by duplex DNA, and the ATP-dependent hybridization of homologous single-stranded DNAs. It interacts with LexA causing its activation and leading to its autocatalytic cleavage; Belongs to the RecA family.	0.940