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COFACTOR result for job id 76405

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>76405 (371 residues)
MPKTKKDLGINKEELLNQVVNNRYKLIKYLNSGAFAVVFKALDLDASVLEKKDVFVAVKI
ILKAKNKNIETIKKRLFLETNTFAKLSFSKNIVKMKDVFSWQNYYVIVMELIEGADLSKK
FNAYNNVLSNKEFLYYFLQITKGLKEIHDNNIIHRDVKPANILITNDSKVRISDFGISKI
KSIILDDHHNHISPGTPRYTAPEQFINFESRKDAFYFESDIYSIGVIMYEFLTGSMLYLN
YGSNHTSSKEKERTNFQQHILKDITRPREINPNISQALENIIMKCLAKDYKNRYHRFDQI
IEDLEQAKQQPDVNIDFPNMWWEDENYLNIKNNNTLKYKYFFKNTNFKYFLFWISIVISL
FIIFLIVLILK

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	3q5iA	0.72	3.02	0.222	0.803	Download
2	3lijA	0.72	3.23	0.213	0.809	Download
3	3hx4A	0.71	3.34	0.211	0.809	Download
4	6c9dA	0.70	3.01	0.249	0.774	Download
5	3f69B	0.69	1.97	0.288	0.736	Download
6	2owbA	0.69	2.04	0.221	0.739	Download
7	2acxA	0.69	2.97	0.164	0.768	Download
8	2y94A	0.69	3.22	0.220	0.776	Download
9	4tnbA	0.69	3.08	0.167	0.771	Download
10	3c4wB	0.69	3.11	0.181	0.771	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:0003824	1.00	catalytic activity
GO:0016301	0.98	kinase activity
GO:0004672	0.97	protein kinase activity
GO:1901363	0.92	heterocyclic compound binding
GO:0097159	0.92	organic cyclic compound binding
GO:0035639	0.91	purine ribonucleoside triphosphate binding
GO:0032555	0.91	purine ribonucleotide binding
GO:0030554	0.91	adenyl nucleotide binding
GO:0004674	0.91	protein serine/threonine kinase activity
GO:0005524	0.90	ATP binding

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:

[0.4,0.5)

[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	1.00	cellular process
GO:0071704	0.99	organic substance metabolic process
GO:0044238	0.99	primary metabolic process
GO:0044237	0.99	cellular metabolic process
GO:0044267	0.98	cellular protein metabolic process
GO:0043412	0.98	macromolecule modification
GO:0006796	0.98	phosphate-containing compound metabolic process
GO:0006468	0.97	protein phosphorylation
GO:0065007	0.79	biological regulation
GO:0050789	0.78	regulation of biological process
GO:0050794	0.76	regulation of cellular process
GO:0044699	0.72	single-organism process
GO:0044763	0.70	single-organism cellular process
GO:0006915	0.60	apoptotic process
GO:0007165	0.58	signal transduction
GO:1901576	0.56	organic substance biosynthetic process
GO:0044249	0.55	cellular biosynthetic process
GO:0006807	0.53	nitrogen compound metabolic process

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:0044464	1.00	cell part
GO:0044424	0.97	intracellular part
GO:0005737	0.80	cytoplasm
GO:0043226	0.79	organelle
GO:0043229	0.78	intracellular organelle
GO:0044444	0.77	cytoplasmic part
GO:0043227	0.76	membrane-bounded organelle
GO:0043231	0.75	intracellular membrane-bounded organelle
GO:0016020	0.69	membrane
GO:0005634	0.65	nucleus
GO:0044422	0.57	organelle part
GO:0044446	0.55	intracellular organelle part
GO:0005829	0.55	cytosol

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	0.338	2bfyB	0.654	2.52	0.187	0.722	2.7.11.1	30,59,119,163
2	0.161	1ql6A	0.682	2.46	0.236	0.739	2.7.11.19 2.7.1.38	NA
3	0.144	2zv2A	0.636	2.13	0.252	0.685	2.7.11.17	NA
4	0.144	3eqrB	0.655	2.45	0.204	0.717	2.7.10.2	NA
5	0.142	3d5uA	0.689	2.14	0.208	0.739	2.7.11.21	59

	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	0.66	3f69A	0.675	1.57	0.289	0.704	1.48	XDR	Download	30,31,38,57,59,109,110,111,112,114,116,160,161,163,173,174
2	0.58	3oroA	0.644	2.18	0.294	0.687	1.04	AGS	Download	30,31,32,33,34,35,36,38,57,59,93,109,110,112,116,158,173
3	0.36	3kb7A	0.693	1.92	0.228	0.733	1.15	071	Download	30,38,57,59,109,110,112,113,115,116,119,162,174
4	0.36	2owbA	0.694	2.04	0.221	0.739	1.21	626	Download	28,29,30,32,33,36,37,38,57,59,110,112,113,115,163
5	0.33	3d5xA	0.672	2.02	0.212	0.717	1.12	KWT	Download	32,33,36,38,57,59,93,109,110,163

	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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