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COFACTOR result for job id 76330

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

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>76330 (132 residues)
METKISFSKKRKLLIQTFYKYQLLNASIDYIHQDILDDVQNINNKDVLFEIEQIAKKQTD
LINHININVSSSWKWDRIPAVIRAILIVGTYEILYTNTPKPVTINEMVKYVKEIEPDFDY
KFVNAVLDKLVK

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	1eyvB	0.90	1.34	0.238	0.955	Download
2	1tzwA	0.89	1.44	0.242	0.955	Download
3	6govB	0.85	2.10	0.233	0.970	Download
4	2jr0A	0.81	2.12	0.180	0.970	Download
5	1sqfA	0.77	2.24	0.165	0.917	Download
6	2b9eA2	0.45	3.81	0.025	0.674	Download
7	2rfoA1	0.39	4.30	0.065	0.629	Download
8	1w6jA	0.37	4.95	0.054	0.674	Download
9	3sc6A	0.36	4.46	0.061	0.561	Download
10	4zn6A1	0.35	4.43	0.087	0.583	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	0.95	catalytic activity
GO:0016740	0.85	transferase activity
GO:0016741	0.79	transferase activity, transferring one-carbon groups
GO:1901363	0.73	heterocyclic compound binding
GO:0097159	0.73	organic cyclic compound binding
GO:0008757	0.71	S-adenosylmethionine-dependent methyltransferase activity
GO:0008173	0.71	RNA methyltransferase activity
GO:0003676	0.71	nucleic acid binding
GO:0008649	0.70	rRNA methyltransferase activity
GO:0003723	0.70	RNA binding
GO:0009383	0.67	rRNA (cytosine-C5-)-methyltransferase activity

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	0.96	cellular process
GO:0071704	0.92	organic substance metabolic process
GO:0044238	0.91	primary metabolic process
GO:0044237	0.91	cellular metabolic process
GO:0006807	0.91	nitrogen compound metabolic process
GO:0034641	0.89	cellular nitrogen compound metabolic process
GO:0043170	0.88	macromolecule metabolic process
GO:0006139	0.87	nucleobase-containing compound metabolic process
GO:0090304	0.84	nucleic acid metabolic process
GO:0044260	0.83	cellular macromolecule metabolic process
GO:0016070	0.79	RNA metabolic process
GO:0034660	0.74	ncRNA metabolic process
GO:0009451	0.73	RNA modification
GO:0001510	0.72	RNA methylation
GO:0000154	0.71	rRNA modification
GO:0031167	0.70	rRNA methylation
GO:0070475	0.69	rRNA base methylation
GO:0065007	0.68	biological regulation
GO:0050794	0.66	regulation of cellular process
GO:0060255	0.64	regulation of macromolecule metabolic process
GO:0031323	0.64	regulation of cellular metabolic process
GO:0006355	0.63	regulation of transcription, DNA-templated
GO:0051128	0.62	regulation of cellular component organization
GO:0031564	0.61	transcription antitermination

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:0005829	0.99	cytosol
GO:0005737	0.54	cytoplasm

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	2cyaA	0.548	3.75	0.054	0.841	6.1.1.1	74
2	0.060	2cybA	0.562	3.63	0.053	0.849	6.1.1.1	4
3	0.060	2zufA	0.567	4.02	0.082	0.917	6.1.1.19	NA
4	0.060	1j09A	0.538	3.64	0.053	0.818	6.1.1.17	NA
5	0.060	2x1lA	0.574	3.68	0.084	0.871	6.1.1.10	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	0.03	1sqfA	0.765	2.24	0.165	0.917	0.35	SAM	Download	85,86,87,88,114
2	0.02	3a04A	0.578	3.83	0.102	0.894	0.37	SF4	Download	52,54,55,84,85,88
3	0.01	3a040	0.578	3.83	0.102	0.894	0.21	III	Download	21,22,54,55,56,79,80,82,83,86
4	0.01	2zueA	0.567	4.02	0.082	0.917	0.11	ANP	Download	69,87,88
5	0.01	1jikA	0.564	3.72	0.035	0.864	0.19	545	Download	22,58,83,87,90
6	0.01	1gaxA	0.577	3.86	0.065	0.901	0.13	VAA	Download	83,84,88
7	0.01	3ts1A	0.573	3.83	0.069	0.879	0.11	TYA	Download	85,89,92,102,106
8	0.01	1x8xA	0.573	3.82	0.060	0.879	0.16	TYR	Download	88,91,100,106
9	0.01	2yxn0	0.573	3.82	0.060	0.879	0.25	III	Download	47,48,50,51,52,56,58,59,85,88,91
10	0.01	1vbnB	0.571	3.76	0.060	0.871	0.14	YSA	Download	84,88,91

	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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