gidB 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:
some 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 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:

Neighborhood

Gene Fusion

Cooccurence

Coexpression

Experiments

Databases

Textmining

[Homology]

Score

gidB

Ribosomal RNA small subunit methyltransferase G; Specifically methylates the N7 position of guanine in position 527 of 16S rRNA (218 aa)

Predicted Functional Partners:

gidA

0.993

trmE

0.919

DVU_1768

0.870

glnS

0.783

gyrA

0.776

hisA

0.739

acpP

0.738

polA

0.707

rnpA

0.673

yidC

0.661

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 Hildenborough, 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:

download

file format is 'PNG': portable network graphic

... as a high-resolution bitmap:

download

same PNG format, but resolution at 400 dpi

... as a vector graphic:

download

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

... as simple tabular text output:

download

TSV: tab separated values - can be opened in Excel

... as an XML summary:

download

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

... 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 annotated functions of the network proteins

Browse interactions in tabular form:

node1	node2	node1 accession	node2 accession	node1 annotation	node2 annotation	score
DVU_1768	gidA	DVU_1768	DVU_1828	Identified by match to protein family HMM TIGR00231	tRNA uridine 5-carboxymethylaminomethyl modification enzyme MnmG; NAD-binding protein involved in the addition of a carboxymethylaminomethyl (cmnm) group at the wobble position (U34) of certain tRNAs, forming tRNA-cmnm(5)s(2)U34; Belongs to the MnmG family	0.900
DVU_1768	gidB	DVU_1768	DVU_1250	Identified by match to protein family HMM TIGR00231	Ribosomal RNA small subunit methyltransferase G; Specifically methylates the N7 position of guanine in position 527 of 16S rRNA	0.870
DVU_1768	polA	DVU_1768	DVU_0496	Identified by match to protein family HMM TIGR00231	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	0.608
DVU_1768	rnpA	DVU_1768	DVU_1075	Identified by match to protein family HMM TIGR00231	Ribonuclease P protein component; RNaseP catalyzes the removal of the 5’-leader sequence from pre-tRNA to produce the mature 5’-terminus. It can also cleave other RNA substrates such as 4.5S RNA. The protein component plays an auxiliary but essential role in vivo by binding to the 5’-leader sequence and broadening the substrate specificity of the ribozyme	0.587
acpP	gidB	DVU_1205	DVU_1250	Acyl carrier protein; Carrier of the growing fatty acid chain in fatty acid biosynthesis	Ribosomal RNA small subunit methyltransferase G; Specifically methylates the N7 position of guanine in position 527 of 16S rRNA	0.738
acpP	glnS	DVU_1205	DVU_2951	Acyl carrier protein; Carrier of the growing fatty acid chain in fatty acid biosynthesis	Glutamine--tRNA ligase; Identified by similarity to SP-P00962; match to protein family HMM PF00749; match to protein family HMM PF03950; match to protein family HMM TIGR00440	0.776
acpP	hisA	DVU_1205	DVU_1038	Acyl carrier protein; Carrier of the growing fatty acid chain in fatty acid biosynthesis	1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase; Identified by similarity to SP-O35006; match to protein family HMM PF00977	0.760
acpP	polA	DVU_1205	DVU_0496	Acyl carrier protein; Carrier of the growing fatty acid chain in fatty acid biosynthesis	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	0.571
gidA	DVU_1768	DVU_1828	DVU_1768	tRNA uridine 5-carboxymethylaminomethyl modification enzyme MnmG; NAD-binding protein involved in the addition of a carboxymethylaminomethyl (cmnm) group at the wobble position (U34) of certain tRNAs, forming tRNA-cmnm(5)s(2)U34; Belongs to the MnmG family	Identified by match to protein family HMM TIGR00231	0.900
gidA	gidB	DVU_1828	DVU_1250	tRNA uridine 5-carboxymethylaminomethyl modification enzyme MnmG; NAD-binding protein involved in the addition of a carboxymethylaminomethyl (cmnm) group at the wobble position (U34) of certain tRNAs, forming tRNA-cmnm(5)s(2)U34; Belongs to the MnmG family	Ribosomal RNA small subunit methyltransferase G; Specifically methylates the N7 position of guanine in position 527 of 16S rRNA	0.993
gidA	gyrA	DVU_1828	DVU_0004	tRNA uridine 5-carboxymethylaminomethyl modification enzyme MnmG; NAD-binding protein involved in the addition of a carboxymethylaminomethyl (cmnm) group at the wobble position (U34) of certain tRNAs, forming tRNA-cmnm(5)s(2)U34; Belongs to the MnmG family	DNA gyrase subunit A; A type II topoisomerase that negatively supercoils closed circular double-stranded (ds) DNA in an ATP-dependent manner to modulate DNA topology and maintain chromosomes in an underwound state. Negative supercoiling favors strand separation, and DNA replication, transcription, recombination and repair, all of which involve strand separation. Also able to catalyze the interconversion of other topological isomers of dsDNA rings, including catenanes and knotted rings. Type II topoisomerases break and join 2 DNA strands simultaneously in an ATP-dependent manner	0.545
gidA	polA	DVU_1828	DVU_0496	tRNA uridine 5-carboxymethylaminomethyl modification enzyme MnmG; NAD-binding protein involved in the addition of a carboxymethylaminomethyl (cmnm) group at the wobble position (U34) of certain tRNAs, forming tRNA-cmnm(5)s(2)U34; Belongs to the MnmG family	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	0.771
gidA	rnpA	DVU_1828	DVU_1075	tRNA uridine 5-carboxymethylaminomethyl modification enzyme MnmG; NAD-binding protein involved in the addition of a carboxymethylaminomethyl (cmnm) group at the wobble position (U34) of certain tRNAs, forming tRNA-cmnm(5)s(2)U34; Belongs to the MnmG family	Ribonuclease P protein component; RNaseP catalyzes the removal of the 5’-leader sequence from pre-tRNA to produce the mature 5’-terminus. It can also cleave other RNA substrates such as 4.5S RNA. The protein component plays an auxiliary but essential role in vivo by binding to the 5’-leader sequence and broadening the substrate specificity of the ribozyme	0.832
gidA	trmE	DVU_1828	DVU_1079	tRNA uridine 5-carboxymethylaminomethyl modification enzyme MnmG; NAD-binding protein involved in the addition of a carboxymethylaminomethyl (cmnm) group at the wobble position (U34) of certain tRNAs, forming tRNA-cmnm(5)s(2)U34; Belongs to the MnmG family	tRNA modification GTPase MnmE; Exhibits a very high intrinsic GTPase hydrolysis rate. Involved in the addition of a carboxymethylaminomethyl (cmnm) group at the wobble position (U34) of certain tRNAs, forming tRNA- cmnm(5)s(2)U34; Belongs to the TRAFAC class TrmE-Era-EngA-EngB-Septin- like GTPase superfamily. TrmE GTPase family	0.989
gidA	yidC	DVU_1828	DVU_1077	tRNA uridine 5-carboxymethylaminomethyl modification enzyme MnmG; NAD-binding protein involved in the addition of a carboxymethylaminomethyl (cmnm) group at the wobble position (U34) of certain tRNAs, forming tRNA-cmnm(5)s(2)U34; Belongs to the MnmG family	Membrane protein insertase YidC; Required for the insertion and/or proper folding and/or complex formation of integral membrane proteins into the membrane. Involved in integration of membrane proteins that insert both dependently and independently of the Sec translocase complex, as well as at least some lipoproteins. Aids folding of multispanning membrane proteins	0.784
gidB	DVU_1768	DVU_1250	DVU_1768	Ribosomal RNA small subunit methyltransferase G; Specifically methylates the N7 position of guanine in position 527 of 16S rRNA	Identified by match to protein family HMM TIGR00231	0.870
gidB	acpP	DVU_1250	DVU_1205	Ribosomal RNA small subunit methyltransferase G; Specifically methylates the N7 position of guanine in position 527 of 16S rRNA	Acyl carrier protein; Carrier of the growing fatty acid chain in fatty acid biosynthesis	0.738
gidB	gidA	DVU_1250	DVU_1828	Ribosomal RNA small subunit methyltransferase G; Specifically methylates the N7 position of guanine in position 527 of 16S rRNA	tRNA uridine 5-carboxymethylaminomethyl modification enzyme MnmG; NAD-binding protein involved in the addition of a carboxymethylaminomethyl (cmnm) group at the wobble position (U34) of certain tRNAs, forming tRNA-cmnm(5)s(2)U34; Belongs to the MnmG family	0.993
gidB	glnS	DVU_1250	DVU_2951	Ribosomal RNA small subunit methyltransferase G; Specifically methylates the N7 position of guanine in position 527 of 16S rRNA	Glutamine--tRNA ligase; Identified by similarity to SP-P00962; match to protein family HMM PF00749; match to protein family HMM PF03950; match to protein family HMM TIGR00440	0.783
gidB	gyrA	DVU_1250	DVU_0004	Ribosomal RNA small subunit methyltransferase G; Specifically methylates the N7 position of guanine in position 527 of 16S rRNA	DNA gyrase subunit A; A type II topoisomerase that negatively supercoils closed circular double-stranded (ds) DNA in an ATP-dependent manner to modulate DNA topology and maintain chromosomes in an underwound state. Negative supercoiling favors strand separation, and DNA replication, transcription, recombination and repair, all of which involve strand separation. Also able to catalyze the interconversion of other topological isomers of dsDNA rings, including catenanes and knotted rings. Type II topoisomerases break and join 2 DNA strands simultaneously in an ATP-dependent manner	0.776

page 1 of 4

Network

Neighborhood

Experiments

Fusion

Textmining

Cooccurrence

Databases

Coexpression

© STRING Consortium 2019

Credits

Access

Info

About