Complex Information

Description: Complex name / short description.

Functional Grouping: Coarse functional classification of cellular function.

Subcellular localisation: Cellular compartment where the complex is mainly localised.

Comments: Miscellaneous comments about the complex or any of its components.

Affinity Purifications: Link to the images of the purification gels (not available yet).

EM rank: Quality of the images obtained by Electron Microscopy: "3" good; "2" acceptable and "1" poor.

Bioinformatics

Component: Individual component name.
Length: Sequence length (AAs).
Status: We have defined three different status for each component: known component found by TAP (known), known components NOT found by TAP (missing) and UNKNOWN component found by TAP (new).
Pfam Doms: PFAM domains identified in this component.
COGs: Information relative to orthologous sequences in different organisms as a link to the Clusters of Orthologous Groups database.
PDB match: Homologous sequences of known structure.
Modellable: Available templates to model this component ("All") or, at least, one of its domains ("Domain").
PFAM Ints: Identified interactions between PFAM domains in this component with other components within the same complex.
SCOP Ints: Identified interactions between SCOP domains in this component with other components within the same complex.

Potential Cross-talk

Confidence: Confidence level placed on this cross-talk prediction from 1(low) to 7(high).

1: structural link
2: both PID >= 25%
3: Zscore >= 2.3
4: Similar broad functional class
5: Experimentally validated
6: 5+2
7: 5+3

Complex1: First complex involved in cross-talk.
Complex2: Second complex involved in cross-talk.
Comp1: First component involved in this interaction.
Comp2: Second component involved in this interaction.
Exp: Experimental validation (i.e. by two-hybrids)
PFAM1: PFAM domain of the first component involved in this interaction.
PFAM2: PFAM domain of the second component involved in this interaction.
Template: Closest PDB structure used as template to model the interaction.
Zscore: InterPreTS Zscore for these two interacting domains.
PID1: Percentage sequence identity shared between the first component and the template.
E-val1: E-value for this hit.
Begin1: First residue of the first component sequence included in the alignment with the template.
End1: Last residue of the first component sequence included in the alignment with the template.
PID2: Percentage sequence identity shared between the second component and the template.
E-val2: E-value for this hit.
Begin2: First residue of the second component sequence included in the alignment with the template.
End2: Last residue of the second component sequence included in the alignment with the template.

Component Information

Alernative names: Different synonyms for this given component, including the sequence identifier, gene and protein names.

Sequence Information

Length: Sequence length (AAs)
MW(kDa): Estimated protein molecular weigth calculated by adding the masses of the individual AAs (- HOH). Obviously, postranslational modifications are no considered.
Status: We have defined three different status for each component: known component found by TAP (i.e. known; "*"), known components NOT found by TAP (i.e. missing; "-") and UNKNOWN component found by TAP (i.e. unexpected; "+")
SMART: Link to SMART (domain architecture database).
SGD: Link to SGD (Yeast genome database).
GRID: Link to GRID (Genetic and physical protein-protein interactions database).
SwP/TrEMBL: Link to SwissProt/TrEMBL database (general sequence database).

PDB hits

PDB: PDB hit (code-chain).
E-val: E-value for this hit.
PID: Percentage sequence identity shared between the component and its homolog of known structure.
Begin: First residue of the component sequence included in the alignment.
End: Last residue of the component sequence included in the alignment.
Overlap: Overlap between the component sequence and the PDB hit.

PFAM domains

PFAM: PFAM domain name.
Seq: Closest homologous sequence to the component in this PFAM domain.
E-val: E-value for this hit.
PID: Percentage sequence identity shared between the component and its homolog classified in PFAM.
Begin: First residue of the component sequence included in the alignment.
End: Last residue of the component sequence included in the alignment.
PDB: Any known 3D structure for this PFAM domain? "x" yes; "-" no.

PFAM interactions

Comp1: First component involved in this interaction.
Comp2: Second component involved in this interaction.
PFAM1: PFAM domain of the first component involved in this interaction.
PFAM2: PFAM domain of the second component involved in this interaction.
Template: Closest PDB structure used as template to model the interaction.
Zscore: InterPreTS Zscore for these two interacting domains.
PID1: Percentage sequence identity shared between the first component and the template.
E-val1: E-value for this hit.
Begin1: First residue of the first component sequence included in the alignment with the template.
End1: Last residue of the first component sequence included in the alignment with the template.
PID2: Percentage sequence identity shared between the second component and the template.
E-val2: E-value for this hit.
Begin2: First residue of the second component sequence included in the alignment with the template.
End2: Last residue of the second component sequence included in the alignment with the template.

SCOP domains

SCOP: SCOP domain identifier.
E-val: E-value for this hit.
PID: Percentage sequence identity shared between the component and its homolog in SCOP.
Begin: First residue of the component sequence included in the alignment.
End: Last residue of the component sequence included in the alignment.

SCOP interactions

Type: Type of interaction identified between structurally similar SCOP domains: between members of the same family ("fam"); same superfamily ("sup") or same fold ("fol").
Comp1: First component involved in this interaction.
Comp2: Second component involved in this interaction.
Hit1: SCOP domain of the first component involved in this interaction.
Hit2: SCOP domain of the second component involved in this interaction.
PID1: Percentage sequence identity shared between the first component and the template.
E-val1: E-value for this hit.
Begin1: First residue of the first component sequence included in the alignment with the template.
End1: Last residue of the first component sequence included in the alignment with the template.
PID2: Percentage sequence identity shared between the second component and the template.
E-val2: E-value for this hit.
Begin2: First residue of the second component sequence included in the alignment with the template.
End2: Last residue of the second component sequence included in the alignment with the template.

Experimentally determined interactions

Comp1: First component involved in this interaction.
Comp2: Second component involved in this interaction.
Method: Experimental method that suggested this interaction (i.e. "two hybrid" - yeast two-hybrid system; "cip" - co-immuno precipitation; "cp" - co-purification.)