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COFACTOR result for job id 76466

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

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>76466 (365 residues)
MSKKIALFGGSFDPIHTDHVNIIKTCYEKLKFDEVWLIPAYLNPFKTKQNSSIVDRLNML
EIIKNKFSYIKIYDYEIKNNKSTPTYQTVKHILKTNQNDHFSFIMGSDQLDRFEEWNNFE
ELIKMIDFKVFKRNEDYNKQVLNKYNLELFEFENNYLSSTDIRNLKHLDKQIKEINDYVN
YNLMYLYERLETQMDQKRYIHCLNVGKMAHDLAIKWNVDPKKALIAGTLHDITKRWSKEQ
SLNYLKTYLPQLINEPYPVWHSYTAYLHLLYDWLIDDKEILSAVFNHTVGSENMSLLDII
VFCADKISIERDYLGVDKLRELCFSDLMLGFKTLLKNQYDLAIKKHGKDNIGSMLIKTIN
YYLKD

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	2ogiA	0.49	1.55	0.306	0.510	Download
2	2o08A	0.47	1.45	0.278	0.493	Download
3	3ccgA	0.47	1.54	0.289	0.493	Download
4	4wsoA	0.47	2.21	0.210	0.510	Download
5	1nuqA	0.47	2.29	0.167	0.510	Download
6	1kaqA	0.47	1.88	0.267	0.493	Download
7	1k4kA	0.46	2.55	0.258	0.510	Download
8	1kqoA	0.46	2.64	0.166	0.510	Download
9	1yumA	0.46	2.58	0.222	0.507	Download
10	2h29A	0.46	2.42	0.280	0.499	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:0070566	0.99	adenylyltransferase activity
GO:0004515	0.98	nicotinate-nucleotide adenylyltransferase activity
GO:0000309	0.91	nicotinamide-nucleotide adenylyltransferase activity
GO:0005524	0.65	ATP binding

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:

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[0.9,1.0]

Biological Process (BP)

GO term	Cscore^GO	Name
GO:0044763	1.00	single-organism cellular process
GO:1901566	0.99	organonitrogen compound biosynthetic process
GO:0009165	0.99	nucleotide biosynthetic process
GO:0009108	0.99	coenzyme biosynthetic process
GO:0034628	0.97	'de novo' NAD biosynthetic process from aspartate

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	0.87	cytoplasm
GO:0043229	0.82	intracellular organelle
GO:0043231	0.70	intracellular membrane-bounded organelle

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	0.304	2h2aA	0.459	2.35	0.280	0.499	2.7.7.18	10,17,19,103,109,160
2	0.277	3e27D	0.469	1.89	0.265	0.496	2.7.7.18	9,22,44,85,103,116,159
3	0.233	1kaqA	0.465	1.88	0.267	0.493	2.7.7.18	9,19,103,159
4	0.222	1k4mB	0.473	2.15	0.253	0.510	2.7.7.18	8,10,85,103,116
5	0.067	1nuuA	0.468	2.31	0.172	0.510	2.7.7.1	11,19,130,155

	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	2qtrB	0.476	1.80	0.268	0.501	1.09	NXX	Download	12,16,19,22,40,45,46,85,103,105,106,108,109,116,117,132,133,155,157
2	0.27	3mlbB	0.452	2.59	0.267	0.493	0.99	LJZ	Download	22,103,104,105,106,109,112,115,116
3	0.14	1kqoD	0.464	2.62	0.166	0.510	0.85	DND	Download	12,18,19,22,40,80,85,105,106,108,109,131,156

	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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