(71 nodes) Ubiquitin-like protein peptidase activity network (Caenorhabditis briggsae)

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:
	josd-1	Protein CBG00486. (173 aa)
	ulp-4	Protein CBR-ULP-4. (385 aa)
	CBG00738	Protein CBG00738; Belongs to the peptidase C19 family. (1242 aa)
	usp-14	Ubiquitin carboxyl-terminal hydrolase. (489 aa)
	CBG01120	Protein CBG01120. (735 aa)
	CBG01315	Protein CBG01315. (402 aa)
	CBG01420	Protein CBG01420. (297 aa)
	csn-6	Protein CBR-CSN-6. (448 aa)
	duo-3	Protein CBR-DUO-3; Belongs to the peptidase C19 family. (891 aa)
	duo-2	Protein CBR-DUO-2; Belongs to the peptidase C19 family. (804 aa)
	CBG03251	Protein CBG03251; Belongs to the peptidase C19 family. (3007 aa)
	CBG02847	Protein CBG02847. (1130 aa)
	ulp-2	Protein CBR-ULP-2. (870 aa)
	eif-3.H	Eukaryotic translation initiation factor 3 subunit H; Component of the eukaryotic translation initiation factor 3 (eIF-3) complex, which is involved in protein synthesis of a specialized repertoire of mRNAs and, together with other initiation factors, stimulates binding of mRNA and methionyl-tRNAi to the 40S ribosome. The eIF-3 complex specifically targets and initiates translation of a subset of mRNAs involved in cell proliferation. (365 aa)
	usp-39	Protein CBG04341. (626 aa)
	CBG04342	Protein CBG04342. (717 aa)
	CBG04349	Protein CBG04349. (185 aa)
	CBG05381	Protein CBG05381; Belongs to the peptidase C19 family. (1009 aa)
	atx-3	Ataxin-3 homolog; Acts as chain editing deubiquitinating enzyme that binds and cleaves 'Lys-48'-linked polyubiquitin chains, with a preference for chains containing four or more ubiquitin molecules thereby modulating protein degradation by the ubiquitin-proteasome pathway. Probably by regulating the IGF-1-insulin-like pathway, regulates lifespan. Regulates germline DNA double-strand-break repair and apoptosis in response to DNA damage by recruiting E4 ubiquitin-protein ligase ufd-2 to DNA repair foci. Interacts with key regulators of transcription and represses transcription. Acts as a [...] (319 aa)
	odr-8	Ufm1-specific protease; Thiol protease which recognizes and hydrolyzes the peptide bond at the C-terminal Gly of ufm-1, a ubiquitin-like modifier protein bound to a number of target proteins. Required, with oct-4, for the localization of a subset of 7 transmembrane domain odorant receptors, including odr-10, to the cilia of olfactory neurons AWA and AWC. Operates in aggregation behavior, and responses to oxygen levels. (588 aa)
	Cbr-srx-5	Protein CBR-SRX-5. (306 aa)
	ulp-5	Protein CBG25370. (484 aa)
	CBG25486	Protein CBG25486. (207 aa)
	CBG22651	Protein CBG22651. (300 aa)
	otub-2	Protein CBG22120. (671 aa)
	CBG21788	Protein CBG21788. (870 aa)
	CBG19435	Protein CBG19435. (333 aa)
	CBG21345	Protein CBG21345. (473 aa)
	ulp-1	Protein CBR-ULP-1. (710 aa)
	otub-4	Protein CBG21043. (419 aa)
	pqn-87	Protein CBR-PQN-87. (1493 aa)
	usp-5	Ubiquitin carboxyl-terminal hydrolase. (795 aa)
	eif-3.f	Protein CBR-EIF-3.F; Belongs to the eIF-3 subunit F family. (251 aa)
	csn-5	Protein CBR-CSN-5. (367 aa)
	usp-46	Ubiquitin carboxyl-terminal hydrolase. (415 aa)
	cyld-1	Protein CBR-CYLD-1. (1175 aa)
	cyk-3	Protein CBR-CYK-3. (1190 aa)
	CBG09100	Protein CBG09100. (1182 aa)
	CBG07652	Protein CBG07652. (470 aa)
	CBG26978	Protein CBG26978. (311 aa)
	usp-33	Ubiquitin carboxyl-terminal hydrolase. (901 aa)
	CBG06402	Protein CBG06402. (1108 aa)
	usp-50	Protein CBG05585; Belongs to the peptidase C19 family. (853 aa)
	srx-10	Protein CBR-SRX-10. (328 aa)
	otub-1	Ubiquitin thioesterase otubain-like; Hydrolase that can remove conjugated ubiquitin from proteins and plays an important regulatory role at the level of protein turnover by preventing degradation. Specifically cleaves 'Lys-48'-linked polyubiquitin (By similarity); Belongs to the peptidase C65 family. (288 aa)
	rpn-8	Protein CBR-RPN-8. (382 aa)
	ubh-4	Ubiquitin carboxyl-terminal hydrolase. (326 aa)
	CBG13344	Protein CBG13344; Belongs to the peptidase C19 family. (1355 aa)
	usp-3	Ubiquitin carboxyl-terminal hydrolase. (538 aa)
	Cbr-immp-2	Protein CBR-IMMP-2. (522 aa)
	CBG15218	Ubiquitin carboxyl-terminal hydrolase. (430 aa)
	CBG16325	Protein CBG16325. (614 aa)
	otub-3	Protein CBG16450. (314 aa)
	prp-8	Protein CBR-PRP-8. (2464 aa)
	CBG16572	Protein CBG16572. (324 aa)
	CBG16582	Protein CBG16582. (228 aa)
	CBG17006	Protein CBG17006. (187 aa)
	CBG17396	Protein CBG17396. (806 aa)
	ubh-3	Ubiquitin carboxyl-terminal hydrolase. (242 aa)
	ubh-1	Ubiquitin carboxyl-terminal hydrolase. (216 aa)
	CBG18955	Protein CBG18955. (148 aa)
	srx-1	Protein CBR-SRX-1. (328 aa)
	CBG19155	Protein CBG19155. (299 aa)
	srx-2	Protein CBR-SRX-2. (334 aa)
	CBG19158	Protein CBG19158. (460 aa)
	CBG27413	Protein CBG27413. (427 aa)
	math-33	Ubiquitin carboxyl-terminal hydrolase 7; Hydrolase that deubiquitinates target proteins. (1129 aa)
	CBG23689	Protein CBG23689. (207 aa)
	rpn-11	Protein CBR-RPN-11. (312 aa)
	CBG24105	Protein CBG24105. (316 aa)
	usp-48	Protein CBR-USP-48; Belongs to the peptidase C19 family. (1264 aa)

Your Current Organism:

Caenorhabditis briggsae

NCBI taxonomy Id: 6238
Other names: C. briggsae, Caenorhabditis briggsae AF16

Send network to Cytoscape

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 protiens in your network

Browse interactions in tabular form:

node1	node2	node1 accession	node2 accession	node1 annotation	node2 annotation	score
CBG00738	CBG01315	A8WN65	A8WQ44	Protein CBG00738; Belongs to the peptidase C19 family.	Protein CBG01315.	0.515
CBG00738	CBG02847	A8WN65	A8WTE0	Protein CBG00738; Belongs to the peptidase C19 family.	Protein CBG02847.	0.404
CBG00738	CBG05381	A8WN65	A8WZR0	Protein CBG00738; Belongs to the peptidase C19 family.	Protein CBG05381; Belongs to the peptidase C19 family.	0.404
CBG00738	CBG15218	A8WN65	A8XLN0	Protein CBG00738; Belongs to the peptidase C19 family.	Ubiquitin carboxyl-terminal hydrolase.	0.513
CBG00738	CBG21788	A8WN65	A8Y0H4	Protein CBG00738; Belongs to the peptidase C19 family.	Protein CBG21788.	0.404
CBG00738	cyk-3	A8WN65	A8X800	Protein CBG00738; Belongs to the peptidase C19 family.	Protein CBR-CYK-3.	0.404
CBG00738	math-33	A8WN65	Q60MK8	Protein CBG00738; Belongs to the peptidase C19 family.	Ubiquitin carboxyl-terminal hydrolase 7; Hydrolase that deubiquitinates target proteins.	0.769
CBG00738	otub-3	A8WN65	A8XP37	Protein CBG00738; Belongs to the peptidase C19 family.	Protein CBG16450.	0.606
CBG00738	usp-14	A8WN65	A8WP63	Protein CBG00738; Belongs to the peptidase C19 family.	Ubiquitin carboxyl-terminal hydrolase.	0.606
CBG00738	usp-33	A8WN65	A8X475	Protein CBG00738; Belongs to the peptidase C19 family.	Ubiquitin carboxyl-terminal hydrolase.	0.403
CBG00738	usp-5	A8WN65	A8XXG5	Protein CBG00738; Belongs to the peptidase C19 family.	Ubiquitin carboxyl-terminal hydrolase.	0.798
CBG00738	usp-50	A8WN65	A8X076	Protein CBG00738; Belongs to the peptidase C19 family.	Protein CBG05585; Belongs to the peptidase C19 family.	0.659
CBG01120	rpn-8	A8WPL7	A8XEJ1	Protein CBG01120.	Protein CBR-RPN-8.	0.411
CBG01315	CBG00738	A8WQ44	A8WN65	Protein CBG01315.	Protein CBG00738; Belongs to the peptidase C19 family.	0.515
CBG01315	otub-3	A8WQ44	A8XP37	Protein CBG01315.	Protein CBG16450.	0.454
CBG01315	usp-14	A8WQ44	A8WP63	Protein CBG01315.	Ubiquitin carboxyl-terminal hydrolase.	0.470
CBG01315	usp-5	A8WQ44	A8XXG5	Protein CBG01315.	Ubiquitin carboxyl-terminal hydrolase.	0.516
CBG01420	rpn-8	A8WQD6	A8XEJ1	Protein CBG01420.	Protein CBR-RPN-8.	0.411
CBG02847	CBG00738	A8WTE0	A8WN65	Protein CBG02847.	Protein CBG00738; Belongs to the peptidase C19 family.	0.404
CBG02847	cyld-1	A8WTE0	A8XA08	Protein CBG02847.	Protein CBR-CYLD-1.	0.640