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COFACTOR result for job id 76529

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>76529 (145 residues)
MKKLITILSSFGLVITTGTTAVACKNNQPSSLKPTAEDQNTSLTSTPENGELSSTGSIQN
KEEEVTKIKGQLEKLKESEQKAKDLLKQIEEGNKKAKEATDQEKIKNELEKLNAQKPEVE
KALKQIEEIKKGLEAKLKSLENKTN

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	1qoyA	0.65	3.56	0.100	0.897	Download
2	4ui9I	0.64	3.63	0.085	0.869	Download
3	6a93A	0.64	3.50	0.103	0.855	Download
4	2d4yA	0.61	3.44	0.070	0.814	Download
5	6ezvX	0.61	4.08	0.092	0.890	Download
6	6g9lA1	0.61	3.49	0.048	0.855	Download
7	4ib4A	0.61	3.49	0.079	0.835	Download
8	6el1O	0.61	3.98	0.093	0.862	Download
9	5tjvA	0.60	3.88	0.049	0.862	Download
10	5vjsA	0.60	3.73	0.078	0.855	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:1901363	0.38	heterocyclic compound binding
GO:0097159	0.38	organic cyclic compound binding
GO:0019899	0.34	enzyme binding
GO:0003676	0.34	nucleic acid binding
GO:0003723	0.32	RNA 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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[0.9,1.0]

Biological Process (BP)

GO term	Cscore^GO	Name
GO:0009987	0.91	cellular process
GO:0044699	0.67	single-organism process
GO:0065007	0.66	biological regulation
GO:0050789	0.66	regulation of biological process
GO:0050794	0.64	regulation of cellular process
GO:0044763	0.64	single-organism cellular 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:0032991	0.93	macromolecular complex
GO:0044424	0.84	intracellular part
GO:0044425	0.73	membrane part
GO:0016021	0.66	integral component of membrane
GO:0043234	0.62	protein complex

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	0.067	1cxzB	0.465	2.83	0.105	0.566	2.7.11.13	NA
2	0.066	1wcrA	0.467	3.41	0.081	0.634	2.7.1.69	NA
3	0.060	2iukA	0.513	4.45	0.049	0.821	1.13.11.12	NA
4	0.060	1j3uA	0.524	3.70	0.078	0.745	4.3.1.1	NA
5	0.060	1rsrB	0.546	4.23	0.055	0.841	1.17.4.1	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:

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	2j68A	0.559	4.02	0.112	0.828	0.26	GDP	Download	30,31,32
2	0.01	1biqB	0.524	4.18	0.101	0.841	0.21	UUU	Download	13,20,118,123
3	0.01	2bu8A	0.532	3.16	0.028	0.731	0.23	ADP	Download	30,71,72,74,75
4	0.01	2bu6A	0.498	3.34	0.065	0.697	0.36	TF2	Download	126,129,133
5	0.01	2w6dB	0.445	4.55	0.045	0.697	0.27	CPL	Download	74,75,76,78,79,82,83,86,87,90
6	0.01	2bu7A	0.529	3.24	0.038	0.731	0.37	TF3	Download	19,21,22,68,71,72,75
7	0.01	3crlA	0.546	3.04	0.047	0.731	0.24	ANP	Download	18,68,69,70,73,74,75
8	0.01	2bu2A	0.500	3.33	0.046	0.697	0.39	TF1	Download	18,129,132
9	0.01	2w6dB	0.445	4.55	0.045	0.697	0.28	CPL	Download	71,72,74,75,76,79,81,82,85,88
10	0.01	3o6xA	0.568	4.01	0.063	0.814	0.13	ADP	Download	71,134,136

	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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