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COFACTOR result for job id 76676

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>76676 (142 residues)
MAKKITRVAKLEFMAMQAKPGAELASLGINMPAFTREFNDATKDRAGDVVPVVITAYDDK
SFDFVLKTTPTAYMLKKVAKIEKGASNSRTQTVATVTLDDIRSIAEYKMPDLNANTIEAA
MKQVIGTAKNMGIKVTGMEDFK

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	3bboK	0.85	1.64	0.434	0.930	Download
2	5o60J	0.84	1.30	0.465	0.908	Download
3	2aw4I	0.82	1.88	0.353	0.937	Download
4	3cf5F	0.82	2.13	0.380	0.937	Download
5	2k3fA	0.81	2.29	0.496	0.944	Download
6	3j21H	0.64	2.98	0.280	0.852	Download
7	3j39K	0.60	3.64	0.048	0.880	Download
8	3jywK	0.58	4.01	0.141	0.901	Download
9	2qa4I	0.53	3.53	0.252	0.775	Download
10	2fowA	0.45	1.77	0.493	0.514	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:0019843	1.00	rRNA binding
GO:0003735	1.00	structural constituent of ribosome
GO:0003824	0.50	catalytic activity

Download full result of the above consensus prediction.

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(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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[0.6,0.7)

[0.7,0.8)

[0.8,0.9)

[0.9,1.0]

Biological Process (BP)

GO term	Cscore^GO	Name
GO:0044238	1.00	primary metabolic process
GO:0043170	1.00	macromolecule metabolic process
GO:0034641	1.00	cellular nitrogen compound metabolic process
GO:0016043	1.00	cellular component organization
GO:0006412	0.99	translation
GO:0000027	0.99	ribosomal large subunit assembly

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:0044444	1.00	cytoplasmic part
GO:0030529	1.00	intracellular ribonucleoprotein complex
GO:0044446	0.99	intracellular organelle part
GO:0015934	0.98	large ribosomal subunit
GO:0043226	0.86	organelle
GO:0043229	0.85	intracellular organelle
GO:0043232	0.80	intracellular non-membrane-bounded organelle
GO:0044445	0.72	cytosolic part
GO:0022625	0.67	cytosolic large ribosomal subunit
GO:0005840	0.65	ribosome
GO:0044429	0.56	mitochondrial part
GO:0005762	0.50	mitochondrial 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	2pffB	0.491	4.79	0.061	0.824	2.3.1.86	70,76
2	0.060	2ywvA	0.450	4.27	0.058	0.697	6.3.2.6	10
3	0.060	2vsfA	0.448	5.39	0.060	0.845	3.6.4.12	125
4	0.060	2qe7A	0.451	4.30	0.046	0.725	3.6.1.34	NA
5	0.060	3lmdA	0.455	4.79	0.073	0.775	2.5.1.30	37

	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:

Rank	Cscore^LB	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	BS-score	Lig. Name	Download Complex	Predicted binding site residues
1	0.08	2nxn1	0.824	1.89	0.410	0.944	1.35	III	Download	10,11,12,14,17,21,22,23,32,36,37,39,40,41,43,44,70,72,76,86,130,131
2	0.01	3aq0B	0.482	4.49	0.079	0.789	0.68	PPV	Download	76,77,83,132
3	0.01	3m6gA	0.360	5.62	0.062	0.711	0.60	LO3	Download	125,128,129,132

	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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