(5 nodes) ATP dependent DNA ligase domain, and PCNA complex network (Verticillium nonalfalfae)

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:
	D7B24_000881	DNA ligase. (860 aa)
	D7B24_008311	DNA ligase. (893 aa)
	D7B24_008797	Vezatin domain-containing protein. (615 aa)
	FEN1	Flap endonuclease 1; Structure-specific nuclease with 5'-flap endonuclease and 5'- 3' exonuclease activities involved in DNA replication and repair. During DNA replication, cleaves the 5'-overhanging flap structure that is generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment. It enters the flap from the 5'-end and then tracks to cleave the flap base, leaving a nick for ligation. Also involved in the long patch base excision repair (LP-BER) pathway, by cleaving within the apurinic/apyrimidinic (AP) site- terminated flap. Acts as [...] (394 aa)
	D7B24_004996	Endo/exonuclease/phosphatase domain-containing protein. (550 aa)

Your Current Organism:

Verticillium nonalfalfae

NCBI taxonomy Id: 1051616
Other names: CBS 130339, NRRL 54791, PD592, UC 1953898, V. nonalfalfae, Verticillium sp. PI-2011d

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 proteins in your network

Browse interactions in tabular form:

node1	node2	node1 accession	node2 accession	node1 annotation	node2 annotation	score
D7B24_000881	D7B24_004996	A0A3M9Y270	A0A3M9YMU6	DNA ligase.	Endo/exonuclease/phosphatase domain-containing protein.	0.794
D7B24_000881	D7B24_008311	A0A3M9Y270	A0A3M9Y5B1	DNA ligase.	DNA ligase.	0.931
D7B24_000881	D7B24_008797	A0A3M9Y270	A0A3M9Y691	DNA ligase.	Vezatin domain-containing protein.	0.945
D7B24_000881	FEN1	A0A3M9Y270	A0A3M9YJU3	DNA ligase.	Flap endonuclease 1; Structure-specific nuclease with 5'-flap endonuclease and 5'- 3' exonuclease activities involved in DNA replication and repair. During DNA replication, cleaves the 5'-overhanging flap structure that is generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment. It enters the flap from the 5'-end and then tracks to cleave the flap base, leaving a nick for ligation. Also involved in the long patch base excision repair (LP-BER) pathway, by cleaving within the apurinic/apyrimidinic (AP) site- terminated flap. Acts as [...]	0.963
D7B24_004996	D7B24_000881	A0A3M9YMU6	A0A3M9Y270	Endo/exonuclease/phosphatase domain-containing protein.	DNA ligase.	0.794
D7B24_004996	D7B24_008311	A0A3M9YMU6	A0A3M9Y5B1	Endo/exonuclease/phosphatase domain-containing protein.	DNA ligase.	0.794
D7B24_004996	D7B24_008797	A0A3M9YMU6	A0A3M9Y691	Endo/exonuclease/phosphatase domain-containing protein.	Vezatin domain-containing protein.	0.859
D7B24_004996	FEN1	A0A3M9YMU6	A0A3M9YJU3	Endo/exonuclease/phosphatase domain-containing protein.	Flap endonuclease 1; Structure-specific nuclease with 5'-flap endonuclease and 5'- 3' exonuclease activities involved in DNA replication and repair. During DNA replication, cleaves the 5'-overhanging flap structure that is generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment. It enters the flap from the 5'-end and then tracks to cleave the flap base, leaving a nick for ligation. Also involved in the long patch base excision repair (LP-BER) pathway, by cleaving within the apurinic/apyrimidinic (AP) site- terminated flap. Acts as [...]	0.996
D7B24_008311	D7B24_000881	A0A3M9Y5B1	A0A3M9Y270	DNA ligase.	DNA ligase.	0.931
D7B24_008311	D7B24_004996	A0A3M9Y5B1	A0A3M9YMU6	DNA ligase.	Endo/exonuclease/phosphatase domain-containing protein.	0.794
D7B24_008311	D7B24_008797	A0A3M9Y5B1	A0A3M9Y691	DNA ligase.	Vezatin domain-containing protein.	0.969
D7B24_008311	FEN1	A0A3M9Y5B1	A0A3M9YJU3	DNA ligase.	Flap endonuclease 1; Structure-specific nuclease with 5'-flap endonuclease and 5'- 3' exonuclease activities involved in DNA replication and repair. During DNA replication, cleaves the 5'-overhanging flap structure that is generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment. It enters the flap from the 5'-end and then tracks to cleave the flap base, leaving a nick for ligation. Also involved in the long patch base excision repair (LP-BER) pathway, by cleaving within the apurinic/apyrimidinic (AP) site- terminated flap. Acts as [...]	0.969
D7B24_008797	D7B24_000881	A0A3M9Y691	A0A3M9Y270	Vezatin domain-containing protein.	DNA ligase.	0.945
D7B24_008797	D7B24_004996	A0A3M9Y691	A0A3M9YMU6	Vezatin domain-containing protein.	Endo/exonuclease/phosphatase domain-containing protein.	0.859
D7B24_008797	D7B24_008311	A0A3M9Y691	A0A3M9Y5B1	Vezatin domain-containing protein.	DNA ligase.	0.969
D7B24_008797	FEN1	A0A3M9Y691	A0A3M9YJU3	Vezatin domain-containing protein.	Flap endonuclease 1; Structure-specific nuclease with 5'-flap endonuclease and 5'- 3' exonuclease activities involved in DNA replication and repair. During DNA replication, cleaves the 5'-overhanging flap structure that is generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment. It enters the flap from the 5'-end and then tracks to cleave the flap base, leaving a nick for ligation. Also involved in the long patch base excision repair (LP-BER) pathway, by cleaving within the apurinic/apyrimidinic (AP) site- terminated flap. Acts as [...]	0.984
FEN1	D7B24_000881	A0A3M9YJU3	A0A3M9Y270	Flap endonuclease 1; Structure-specific nuclease with 5'-flap endonuclease and 5'- 3' exonuclease activities involved in DNA replication and repair. During DNA replication, cleaves the 5'-overhanging flap structure that is generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment. It enters the flap from the 5'-end and then tracks to cleave the flap base, leaving a nick for ligation. Also involved in the long patch base excision repair (LP-BER) pathway, by cleaving within the apurinic/apyrimidinic (AP) site- terminated flap. Acts as [...]	DNA ligase.	0.963
FEN1	D7B24_004996	A0A3M9YJU3	A0A3M9YMU6	Flap endonuclease 1; Structure-specific nuclease with 5'-flap endonuclease and 5'- 3' exonuclease activities involved in DNA replication and repair. During DNA replication, cleaves the 5'-overhanging flap structure that is generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment. It enters the flap from the 5'-end and then tracks to cleave the flap base, leaving a nick for ligation. Also involved in the long patch base excision repair (LP-BER) pathway, by cleaving within the apurinic/apyrimidinic (AP) site- terminated flap. Acts as [...]	Endo/exonuclease/phosphatase domain-containing protein.	0.996
FEN1	D7B24_008311	A0A3M9YJU3	A0A3M9Y5B1	Flap endonuclease 1; Structure-specific nuclease with 5'-flap endonuclease and 5'- 3' exonuclease activities involved in DNA replication and repair. During DNA replication, cleaves the 5'-overhanging flap structure that is generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment. It enters the flap from the 5'-end and then tracks to cleave the flap base, leaving a nick for ligation. Also involved in the long patch base excision repair (LP-BER) pathway, by cleaving within the apurinic/apyrimidinic (AP) site- terminated flap. Acts as [...]	DNA ligase.	0.969
FEN1	D7B24_008797	A0A3M9YJU3	A0A3M9Y691	Flap endonuclease 1; Structure-specific nuclease with 5'-flap endonuclease and 5'- 3' exonuclease activities involved in DNA replication and repair. During DNA replication, cleaves the 5'-overhanging flap structure that is generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment. It enters the flap from the 5'-end and then tracks to cleave the flap base, leaving a nick for ligation. Also involved in the long patch base excision repair (LP-BER) pathway, by cleaving within the apurinic/apyrimidinic (AP) site- terminated flap. Acts as [...]	Vezatin domain-containing protein.	0.984