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COFACTOR result for job id 76610

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>76610 (122 residues)
MIQTLSKLKVADNSGAKEVRVIRNLGGSVRKFSGIGDIIICSVISATPGAVIKKGQVVKA
VIVRTTRELRREDGTYIKFSENAAVLIKEDKTPRGTRIFGPIAREIKEAGFAKIASLAPE
VL

Download query sequence and structure

Proteins with similar structure

Top 10 structural analogs in PDB (as identified by TM-align)

Rank	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	Download Alignment
1	1ml5n	0.98	0.59	0.648	1.000	Download
2	2zjrH	0.98	0.63	0.533	1.000	Download
3	3bboM	0.97	0.69	0.504	0.992	Download
4	1vw4I	0.93	1.01	0.387	0.975	Download
5	2otjK	0.90	1.39	0.432	0.967	Download
6	4a17J	0.89	1.43	0.347	0.967	Download
7	3j21J	0.89	1.42	0.398	0.967	Download
8	5an9E	0.88	1.50	0.299	0.959	Download
9	2gyaI	0.86	2.00	0.529	0.992	Download
10	3zf7W	0.84	1.85	0.331	0.967	Download

(a)	Query structure is shown in cartoon, while the structural analog is displayed using backbone trace.
(b)	Ranking of proteins is based on TM-score of the structural alignment between the query structure and known structures in the PDB library.
(c)	RMSD^a is the RMSD between residues that are structurally aligned by TM-align.
(d)	IDEN^a is the percentage sequence identity in the structurally aligned region.
(e)	Cov. represents the coverage of the alignment by TM-align and is equal to the number of structurally aligned residues divided by length of the query protein.

Predicted Gene Ontology (GO) Terms

Molecular Function (MF)

GO term	Cscore^GO	Name
GO:0003735	1.00	structural constituent of ribosome
GO:0070180	0.99	large ribosomal subunit rRNA binding

Download full result of the above consensus prediction.

Click the graph to show a high resolution version.

(a)

Cscore^GO is the confidence score of predicted GO terms. Cscore^GO values range in between [0-1]; where a higher value indicates a better confidence in predicting the function using the template.

(b)

The graph shows the predicted terms within the Gene Ontology hierachy for Molecular Function. Confidently predicted terms are color coded by Cscore^GO:

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[0.5,0.6)

[0.6,0.7)

[0.7,0.8)

[0.8,0.9)

[0.9,1.0]

Biological Process (BP)

GO term	Cscore^GO	Name
GO:0009987	0.99	cellular process
GO:0071704	0.98	organic substance metabolic process
GO:0044237	0.98	cellular metabolic process
GO:0044238	0.97	primary metabolic process
GO:0043170	0.97	macromolecule metabolic process
GO:0034641	0.97	cellular nitrogen compound metabolic process
GO:1901564	0.96	organonitrogen compound metabolic process
GO:0044271	0.96	cellular nitrogen compound biosynthetic process
GO:0034645	0.96	cellular macromolecule biosynthetic process
GO:0006412	0.95	translation
GO:0071840	0.55	cellular component organization or biogenesis
GO:0016043	0.53	cellular component organization

Download full result of the above consensus prediction.

Click the graph to show a high resolution version.

(a)

Cscore^GO is the confidence score of predicted GO terms. Cscore^GO values range in between [0-1]; where a higher value indicates a better confidence in predicting the function using the template.

(b)

The graph shows the predicted terms within the Gene Ontology hierachy for Biological Process. Confidently predicted terms are color coded by Cscore^GO:

[0.4,0.5)

[0.5,0.6)

[0.6,0.7)

[0.7,0.8)

[0.8,0.9)

[0.9,1.0]

Cellular Component (CC)

GO term	Cscore^GO	Name
GO:0005840	1.00	ribosome
GO:0044446	0.98	intracellular organelle part
GO:0044391	0.97	ribosomal subunit
GO:0044445	0.96	cytosolic part
GO:0015934	0.96	large ribosomal subunit
GO:0022625	0.95	cytosolic large ribosomal subunit

Download full result of the above consensus prediction.

Click the graph to show a high resolution version.

(a)

Cscore^GO is the confidence score of predicted GO terms. Cscore^GO values range in between [0-1]; where a higher value indicates a better confidence in predicting the function using the template.

(b)

The graph shows the predicted terms within the Gene Ontology hierachy for Cellular Component. Confidently predicted terms are color coded by Cscore^GO:

[0.4,0.5)

[0.5,0.6)

[0.6,0.7)

[0.7,0.8)

[0.8,0.9)

[0.9,1.0]

Predicted Enzyme Commission (EC) Numbers

Top 5 enzyme homologs in PDB

Rank	Cscore^EC	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	EC Number	Predicted Active Site Residues
1	0.060	2vqyA	0.349	5.22	0.084	0.664	2.3.1.82	NA
2	0.060	3gmaB	0.424	4.74	0.069	0.754	4.1.1.70	NA
3	0.060	2ou2A	0.427	5.16	0.049	0.811	2.3.1.48	NA
4	0.060	2vuaA	0.477	3.93	0.074	0.730	3.4.24.69	91,117
5	0.060	3btaA	0.460	4.15	0.071	0.738	3.4.24.69	NA

	Click on the radio buttons to visualize predicted active site residues.
(a)	Cscore^EC is the confidence score for the Enzyme Commission (EC) number prediction. Cscore^EC values range in between [0-1]; where a higher score indicates a more reliable EC number prediction.
(b)	TM-score is a measure of global structural similarity between query and template protein.
(c)	RMSD^a is the RMSD between residues that are structurally aligned by TM-align.
(d)	IDEN^a is the percentage sequence identity in the structurally aligned region.
(e)	Cov. represents the coverage of global structural alignment and is equal to the number of structurally aligned residues divided by length of the query protein.

Predicted Ligand Binding Sites

Template proteins with similar binding site:

Click to view	Rank	Cscore^LB	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	BS-score	Lig. Name	Download Complex	Predicted binding site residues
	1	0.01	3r4sA	0.446	4.38	0.109	0.770	0.40	SLB	Download	12,13,14,95,100,115
	2	0.01	1i5o3	0.278	5.30	0.065	0.582	0.42	III	Download	93,94,95,114

	Click on the radio buttons to visualize predicted binding site and residues.
(a)	Cscore^LB is the confidence score of predicted binding site. Cscore^LB values range in between [0-1]; where a higher score indicates a more reliable ligand-binding site prediction.
(b)	BS-score is a measure of local similarity (sequence & structure) between template binding site and predicted binding site in the query structure. Based on large scale benchmarking analysis, we have observed that a BS-score >1 reflects a significant local match between the predicted and template binding site.
(c)	TM-score is a measure of global structural similarity between query and template protein.
(d)	RMSD^a the RMSD between residues that are structurally aligned by TM-align.
(e)	IDEN^a is the percentage sequence identity in the structurally aligned region.
(f)	Cov. represents the coverage of global structural alignment and is equal to the number of structurally aligned residues divided by length of the query protein.

[Download result.tar.bz2 for all prediction results]

Reference:

Chengxin Zhang, Peter L Freddolino, and Yang Zhang. COFACTOR: Improved protein function prediction by combining structure, sequence, and protein-protein interaction information. Nucleic Acids Research, 45: W291-299 (2017)
Ambrish Roy, Jianyi Yang, and Yang Zhang. COFACTOR: An accurate comparative algorithm for structure-based protein function annotation. Nucleic Acids Research, 40:W471-W477 (2012).

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