Cphy_2207 protein (Lachnoclostridium phytofermentans)

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

Cphy_2207

KEGG: ssp:SSP1089 FKBP-type peptidyl-prolyl cis-trans isomerase. (345 aa)

Predicted Functional Partners:

rpsF

0.900

rpsG

0.896

rpsD

0.890

rpsU

0.886

rpsK

0.886

rpsH

0.886

rplC

0.886

rpsB

0.885

rplU

0.884

rplN

0.884

Your Current Organism:

Lachnoclostridium phytofermentans

NCBI taxonomy Id: 357809
Other names: Clostridium phytofermentans ISDg, L. phytofermentans ISDg, Lachnoclostridium phytofermentans ISDg

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
Cphy_2207	rplC	Cphy_2207	Cphy_3667	KEGG: ssp:SSP1089 FKBP-type peptidyl-prolyl cis-trans isomerase.	Ribosomal protein L3; One of the primary rRNA binding proteins, it binds directly near the 3'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit; Belongs to the universal ribosomal protein uL3 family.	0.886
Cphy_2207	rplN	Cphy_2207	Cphy_3657	KEGG: ssp:SSP1089 FKBP-type peptidyl-prolyl cis-trans isomerase.	Ribosomal protein L14; Binds to 23S rRNA. Forms part of two intersubunit bridges in the 70S ribosome; Belongs to the universal ribosomal protein uL14 family.	0.884
Cphy_2207	rplU	Cphy_2207	Cphy_2551	KEGG: ssp:SSP1089 FKBP-type peptidyl-prolyl cis-trans isomerase.	Ribosomal protein L21; This protein binds to 23S rRNA in the presence of protein L20; Belongs to the bacterial ribosomal protein bL21 family.	0.884
Cphy_2207	rpsB	Cphy_2207	Cphy_2680	KEGG: ssp:SSP1089 FKBP-type peptidyl-prolyl cis-trans isomerase.	PFAM: ribosomal protein S2; KEGG: bld:BLi01870 ribosomal protein S2; RBL02224; Belongs to the universal ribosomal protein uS2 family.	0.885
Cphy_2207	rpsD	Cphy_2207	Cphy_3640	KEGG: ssp:SSP1089 FKBP-type peptidyl-prolyl cis-trans isomerase.	RNA-binding S4 domain protein; One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the body of the 30S subunit.	0.890
Cphy_2207	rpsF	Cphy_2207	Cphy_3774	KEGG: ssp:SSP1089 FKBP-type peptidyl-prolyl cis-trans isomerase.	Ribosomal protein S6; Binds together with S18 to 16S ribosomal RNA.	0.900
Cphy_2207	rpsG	Cphy_2207	Cphy_0236	KEGG: ssp:SSP1089 FKBP-type peptidyl-prolyl cis-trans isomerase.	Ribosomal protein S7; One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the head domain of the 30S subunit. Is located at the subunit interface close to the decoding center, probably blocks exit of the E-site tRNA; Belongs to the universal ribosomal protein uS7 family.	0.896
Cphy_2207	rpsH	Cphy_2207	Cphy_3653	KEGG: ssp:SSP1089 FKBP-type peptidyl-prolyl cis-trans isomerase.	Ribosomal protein S8; One of the primary rRNA binding proteins, it binds directly to 16S rRNA central domain where it helps coordinate assembly of the platform of the 30S subunit; Belongs to the universal ribosomal protein uS8 family.	0.886
Cphy_2207	rpsK	Cphy_2207	Cphy_3641	KEGG: ssp:SSP1089 FKBP-type peptidyl-prolyl cis-trans isomerase.	Ribosomal protein S11; Located on the platform of the 30S subunit, it bridges several disparate RNA helices of the 16S rRNA. Forms part of the Shine- Dalgarno cleft in the 70S ribosome; Belongs to the universal ribosomal protein uS11 family.	0.886
Cphy_2207	rpsU	Cphy_2207	Cphy_2616	KEGG: ssp:SSP1089 FKBP-type peptidyl-prolyl cis-trans isomerase.	PFAM: ribosomal protein S21; KEGG: cpr:CPR_1995 ribosomal protein S21; Belongs to the bacterial ribosomal protein bS21 family.	0.886
rplC	Cphy_2207	Cphy_3667	Cphy_2207	Ribosomal protein L3; One of the primary rRNA binding proteins, it binds directly near the 3'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit; Belongs to the universal ribosomal protein uL3 family.	KEGG: ssp:SSP1089 FKBP-type peptidyl-prolyl cis-trans isomerase.	0.886
rplC	rplN	Cphy_3667	Cphy_3657	Ribosomal protein L3; One of the primary rRNA binding proteins, it binds directly near the 3'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit; Belongs to the universal ribosomal protein uL3 family.	Ribosomal protein L14; Binds to 23S rRNA. Forms part of two intersubunit bridges in the 70S ribosome; Belongs to the universal ribosomal protein uL14 family.	0.999
rplC	rplU	Cphy_3667	Cphy_2551	Ribosomal protein L3; One of the primary rRNA binding proteins, it binds directly near the 3'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit; Belongs to the universal ribosomal protein uL3 family.	Ribosomal protein L21; This protein binds to 23S rRNA in the presence of protein L20; Belongs to the bacterial ribosomal protein bL21 family.	0.994
rplC	rpsB	Cphy_3667	Cphy_2680	Ribosomal protein L3; One of the primary rRNA binding proteins, it binds directly near the 3'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit; Belongs to the universal ribosomal protein uL3 family.	PFAM: ribosomal protein S2; KEGG: bld:BLi01870 ribosomal protein S2; RBL02224; Belongs to the universal ribosomal protein uS2 family.	0.995
rplC	rpsD	Cphy_3667	Cphy_3640	Ribosomal protein L3; One of the primary rRNA binding proteins, it binds directly near the 3'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit; Belongs to the universal ribosomal protein uL3 family.	RNA-binding S4 domain protein; One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the body of the 30S subunit.	0.996
rplC	rpsF	Cphy_3667	Cphy_3774	Ribosomal protein L3; One of the primary rRNA binding proteins, it binds directly near the 3'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit; Belongs to the universal ribosomal protein uL3 family.	Ribosomal protein S6; Binds together with S18 to 16S ribosomal RNA.	0.992
rplC	rpsG	Cphy_3667	Cphy_0236	Ribosomal protein L3; One of the primary rRNA binding proteins, it binds directly near the 3'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit; Belongs to the universal ribosomal protein uL3 family.	Ribosomal protein S7; One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the head domain of the 30S subunit. Is located at the subunit interface close to the decoding center, probably blocks exit of the E-site tRNA; Belongs to the universal ribosomal protein uS7 family.	0.997
rplC	rpsH	Cphy_3667	Cphy_3653	Ribosomal protein L3; One of the primary rRNA binding proteins, it binds directly near the 3'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit; Belongs to the universal ribosomal protein uL3 family.	Ribosomal protein S8; One of the primary rRNA binding proteins, it binds directly to 16S rRNA central domain where it helps coordinate assembly of the platform of the 30S subunit; Belongs to the universal ribosomal protein uS8 family.	0.998
rplC	rpsK	Cphy_3667	Cphy_3641	Ribosomal protein L3; One of the primary rRNA binding proteins, it binds directly near the 3'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit; Belongs to the universal ribosomal protein uL3 family.	Ribosomal protein S11; Located on the platform of the 30S subunit, it bridges several disparate RNA helices of the 16S rRNA. Forms part of the Shine- Dalgarno cleft in the 70S ribosome; Belongs to the universal ribosomal protein uS11 family.	0.997
rplC	rpsU	Cphy_3667	Cphy_2616	Ribosomal protein L3; One of the primary rRNA binding proteins, it binds directly near the 3'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit; Belongs to the universal ribosomal protein uL3 family.	PFAM: ribosomal protein S21; KEGG: cpr:CPR_1995 ribosomal protein S21; Belongs to the bacterial ribosomal protein bS21 family.	0.922