[back]

COFACTOR result for job id 76464

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

User Input

>76464 (245 residues)
MQTNLKQYLDYLVEFIQQTVKKAKCDGVVVGISGGIDSAVVANLAKLAFPNNYLTVWMPI
YSSQLDYDCANELIKTNQLKNIEVNLEASFDAFKNSFSNLDEKPNLLAISNAKARLRMTT
LYTIAQTKKYLVLGTDNLDEWHIGYFTKYGDGGVDVVPIIHLLKSEVKKAAQILNVPEII
INRKPTAGLWEGQTDEGEIGFSYDLIDSYLLKQNNDPELKKRIDYLHKISKHKRSLAIKP
KKIIR

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	3fiuA	0.96	0.66	0.380	0.967	Download
2	2pz8A	0.93	1.69	0.336	0.988	Download
3	4q16A	0.92	1.74	0.305	0.984	Download
4	1xngB	0.92	1.56	0.322	0.963	Download
5	3q4gA	0.88	1.79	0.287	0.939	Download
6	3hmqA	0.86	2.13	0.294	0.935	Download
7	3p52A	0.82	1.45	0.321	0.857	Download
8	3n05A2	0.82	2.14	0.315	0.878	Download
9	3dlaD	0.82	2.29	0.189	0.894	Download
10	3ilvA2	0.68	1.64	0.193	0.718	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:0016879	1.00	ligase activity, forming carbon-nitrogen bonds
GO:0016884	0.98	carbon-nitrogen ligase activity, with glutamine as amido-N-donor
GO:0003952	0.97	NAD+ synthase (glutamine-hydrolyzing) activity
GO:0008795	0.95	NAD+ synthase activity
GO:0000166	0.94	nucleotide binding
GO:0005524	0.93	ATP binding
GO:0046872	0.90	metal ion binding
GO:0016787	0.65	hydrolase activity
GO:0016810	0.50	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds

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:1901566	1.00	organonitrogen compound biosynthetic process
GO:0009165	1.00	nucleotide biosynthetic process
GO:0019362	0.99	pyridine nucleotide metabolic process
GO:0009435	0.98	NAD biosynthetic process
GO:0043170	0.65	macromolecule metabolic process
GO:0032502	0.63	developmental process
GO:0030435	0.61	sporulation resulting in formation of a cellular spore
GO:0090304	0.58	nucleic acid metabolic process
GO:0044260	0.53	cellular macromolecule 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:0005737	0.96	cytoplasm
GO:0044444	0.68	cytoplasmic part
GO:0005829	0.50	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	0.586	3fiuA	0.957	0.66	0.380	0.967	6.3.1.5	35,37,112,114,118,121,135,140,146,152,188,190,198
2	0.507	2e18B	0.916	1.44	0.384	0.959	6.3.1.5	31,33,118,121,134,140,144,146,152,188,234
3	0.403	2pzbD	0.773	2.46	0.276	0.861	6.3.1.5	31,33,35,37,111,114,118,134,136,150,152,164
4	0.060	2goyD	0.580	3.93	0.078	0.751	1.8.4.8	117
5	0.060	2x3fA	0.498	5.01	0.056	0.718	6.3.2.1	134

	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	0.63	3fiuA	0.957	0.66	0.380	0.967	1.48	AMP	Download	31,32,33,38,56,58,117,135,140,151,186,187
2	0.46	3fiuA	0.957	0.66	0.380	0.967	0.94	POP	Download	33,35,36,37,38,140,185,186
3	0.39	3q4gA	0.881	1.78	0.290	0.943	1.20	CA	Download	33,35,37,38
4	0.23	1kqpA	0.927	1.72	0.328	0.988	1.36	ADJ	Download	30,31,32,33,38,56,57,58,107,111,114,115,117,135,140,145,146,147,148,151,186,187,189,198,232,233
5	0.15	2hmaA	0.595	3.79	0.158	0.759	0.82	SAM	Download	31,32,33,38,56,58,134,135,136
6	0.09	1nsyA	0.927	1.74	0.328	0.988	1.27	ATP	Download	107,111,115,146,147,148,232,233
7	0.07	1xnh0	0.912	1.33	0.330	0.951	1.21	III	Download	11,15,19,23,84,90,108,111,112,115,118,119,120,122,123,126,127,141,148,149,153,154,155,156,157,161,236,237,238

	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]