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COFACTOR result for job id 76545

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>76545 (433 residues)
MTNSSTSDKKTLENFFIKNFKYKLLKSKVNSSVSYLYSSNEKHQVIILNFDNNISFEKEK
EYIIKKVEKQIKKPVNVFHIVIDNDNQLTTKSNLIVLHSSIQTLATDLEPYFKNTNLLVF
NHTIDNELKDDKQPSEEANNKLFTSFLENVKNNKITFSWAVLLILILIPSMLQIVGYFIL
ETNPNSKNVLILAFGGTNWNLTIVGKQWWRIFTYGIAPIKQNGLIVDILSLLILGTSFFS
ISKITEIQLANTKKLILATILSYLILGLFSSSVLPTIYTGGLISTMGIFIGVLLIDVSGS
TTPMAKFSQAKTVVYILILIGFSFFLGDGWTGLLITGTAVILGSAFWGILKVNIKEWAWI
QYVHIFLILAILAISLTFIFLPHLTPALDQHILITLSTYYKKGWFSINSLNKIVNNIGWD
GQFNQFGKFITNF

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	2fxhA	0.42	6.76	0.047	0.667	Download
2	1itkB	0.42	6.83	0.030	0.670	Download
3	2ccdA	0.42	6.67	0.044	0.660	Download
4	6h02A	0.42	7.28	0.043	0.709	Download
5	5whqA	0.42	6.91	0.042	0.674	Download
6	1ub2A	0.42	6.89	0.033	0.667	Download
7	3ut2A	0.42	6.94	0.022	0.672	Download
8	4wz9A	0.41	6.75	0.039	0.651	Download
9	3s5hA	0.40	7.18	0.051	0.663	Download
10	5a9q1	0.39	7.21	0.078	0.654	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:0016787	0.94	hydrolase activity
GO:0004252	0.84	serine-type endopeptidase activity
GO:0019239	0.65	deaminase 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:

[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:0071704	1.00	organic substance metabolic process
GO:0044238	1.00	primary metabolic process
GO:0044237	0.99	cellular metabolic process
GO:0006139	0.98	nucleobase-containing compound metabolic process
GO:0043170	0.95	macromolecule metabolic process
GO:0016485	0.83	protein processing
GO:0090304	0.72	nucleic acid metabolic process
GO:0016070	0.71	RNA metabolic process
GO:0034660	0.68	ncRNA metabolic process
GO:1901564	0.59	organonitrogen compound metabolic process
GO:0044281	0.58	small molecule metabolic process
GO:0006399	0.50	tRNA 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:0044424	1.00	intracellular part
GO:0044444	0.93	cytoplasmic part
GO:0016020	0.87	membrane
GO:0044446	0.86	intracellular organelle part
GO:0005737	0.75	cytoplasm
GO:0044425	0.67	membrane part
GO:0031090	0.60	organelle membrane
GO:0005743	0.55	mitochondrial inner membrane

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	1oacB	0.365	7.31	0.049	0.612	1.4.3.21 1.4.3.6	NA
2	0.060	1ygpA	0.360	6.50	0.027	0.552	2.4.1.1	NA
3	0.060	2ckjA	0.375	7.59	0.044	0.658	1.17.1.4 1.17.3.2	NA
4	0.060	2fxhA	0.421	6.76	0.047	0.667	1.11.1.7 1.11.1.6	NA
5	0.060	1itkB	0.420	6.83	0.030	0.670	1.11.1.6 1.11.1.7	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	1fiqA	0.157	5.40	0.023	0.217	0.68	FES	Download	285,286,287,290,337,341,343
2	0.01	2ckjD	0.336	7.63	0.043	0.582	0.63	FES	Download	266,267,280,281,282,283
3	0.01	2ckjA	0.375	7.59	0.044	0.658	0.60	FES	Download	193,195,196,216
4	0.01	2ckjA	0.375	7.59	0.044	0.658	0.68	FES	Download	265,266,267,336,337,338,339
5	0.01	2ckjD	0.336	7.63	0.043	0.582	0.65	FES	Download	280,281,323,324,332

	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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