[back]

COFACTOR result for job id 76497

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

User Input

>76497 (547 residues)
MKKLELLKNMITSGVNNLYNHYPQIDKLNVFPVPDGDTGTNMNLTATNGYNEVIDVEYES
IGKFLSAFSRGLIMGARGNSGVIFSQIIKGLSLGMNNAKELSVSEWKSGFSKASEIAYKA
VMKPVEGTILTVIRETSEKVSQLADDIDIKDFWKQVVKNANQSLENTPNLLPLLKEVGVV
DSGGYGLVKFLEGIEYYVLNDQIVNKLDKLEVNNGGNVDMQIEEEFGYCTEAIVMLNDDW
INKLQNSVIRDQLQIFGNTSIVVVVDNDILKVHTHSLSPGQVLQFLQQYGDFQTLKIENM
NLQANKQVKNKDQKWKENSDIKTERKLINETAIISVVSSEKQKRYFEDELGIAFAINAGA
KMNPSTEDFLQAIETVDAKTVFLLPNSSNVYLTAKQAEKIENKSKIYVIQTKTIQQGMVA
ALSFDPSLTASKNYSYLSKSFRNVVSFNITKAEKNTTYNGIEIQKDNLLAIVDNNIIGAE
QTLEAIFDKQLSKYIKSKTEIITIFVGGETNEQDLVQLRKFLDEGYDVEYEIFDGGQETY
NLLIAIE

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	2btdA	0.34	2.14	0.147	0.360	Download
2	1un8A2	0.32	1.87	0.134	0.336	Download
3	3cr3A	0.30	2.09	0.138	0.318	Download
4	5gupl	0.26	5.82	0.045	0.355	Download
5	6nbqB	0.25	6.07	0.091	0.358	Download
6	5xtcr	0.25	6.02	0.044	0.356	Download
7	2ongA	0.25	6.04	0.038	0.355	Download
8	4okmA	0.25	5.56	0.049	0.340	Download
9	1n1zA	0.25	5.86	0.033	0.351	Download
10	3v1vA	0.25	5.46	0.080	0.336	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	0.91	catalytic activity
GO:0016740	0.69	transferase activity
GO:0016772	0.61	transferase activity, transferring phosphorus-containing groups
GO:0016301	0.55	kinase activity
GO:0016773	0.54	phosphotransferase activity, alcohol group as acceptor

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:

[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	0.99	cellular process
GO:0071704	0.98	organic substance metabolic process
GO:0044238	0.97	primary metabolic process
GO:0044699	0.95	single-organism process
GO:0044237	0.95	cellular metabolic process
GO:0005975	0.95	carbohydrate metabolic process
GO:0044281	0.90	small molecule metabolic process
GO:0044763	0.88	single-organism cellular process
GO:0044723	0.88	single-organism carbohydrate metabolic process
GO:0044262	0.88	cellular carbohydrate metabolic process
GO:0006071	0.80	glycerol metabolic process
GO:0009056	0.77	catabolic process
GO:0016052	0.76	carbohydrate catabolic process
GO:0044282	0.69	small molecule catabolic process
GO:0044724	0.68	single-organism carbohydrate catabolic process
GO:0044248	0.61	cellular catabolic process
GO:0019563	0.59	glycerol catabolic process
GO:0050896	0.58	response to stimulus
GO:0006807	0.50	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:0005829	1.00	cytosol
GO:0043226	0.67	organelle
GO:0043229	0.66	intracellular organelle
GO:0043231	0.65	intracellular membrane-bounded organelle
GO:0005737	0.62	cytoplasm
GO:0005618	0.52	cell wall

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	3kb9A	0.238	5.20	0.039	0.313	4.2.3.37	NA
2	0.060	1cc1L	0.242	5.89	0.066	0.340	1.12.99.6	NA
3	0.060	1h2rL	0.240	6.04	0.066	0.342	1.12.2.1	136
4	0.060	3g4dA	0.244	5.79	0.071	0.338	4.2.3.13	NA
5	0.060	2fp0B	0.232	5.31	0.072	0.309	3.2.1.143	39,42,46,193

	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	0.07	1un9A	0.320	1.80	0.137	0.331	1.33	ANP	Download	35,37,38,41,79,80,83,120,122,128,129,181,183
2	0.03	2btdA	0.342	2.14	0.147	0.360	1.10	MG	Download	35,37,78
3	0.02	1un8A	0.324	1.87	0.134	0.336	0.99	MYY	Download	10,14,18,45,61,65,68,76,84,88,106,110,194

	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).

[back]