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COFACTOR result for job id 76660

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

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>76660 (280 residues)
MPNLKGLKTEILSVKNISKITNAMQLVASAKLRKISKKVIDTHNYVSEVYSLFNDIISQA
DKSVFLKDSNFETKKTLWIVINSNLGLCGGYNSNVNKLVLQNLKTNDEIFAIGSKAVSFF
KSKKIKIRDQVTNIDINFTNEKAKIISNDLLAMYTNREFDEIKIVYTKFINNVTFEPAII
RIFPIVKSELHFTHKQKIIFEPDADQILNNTISIYINAIIYGTVIESQVSEQASRRTAME
NATNNGQNLEHELSLKYNRQRQGAITQEISEIVSGANAQS

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	6fkfg	0.93	1.62	0.338	0.982	Download
2	5dn6G	0.85	1.77	0.320	0.914	Download
3	4xd7G	0.81	1.58	0.349	0.861	Download
4	5lqxG	0.81	3.08	0.268	0.929	Download
5	5fl7G	0.80	2.98	0.282	0.921	Download
6	3fksG	0.78	3.09	0.262	0.918	Download
7	6f5dG	0.77	3.29	0.179	0.911	Download
8	1e79G	0.75	3.66	0.299	0.896	Download
9	2qe7G	0.74	1.74	0.312	0.789	Download
10	1fs0G	0.71	1.87	0.291	0.761	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	0.99	catalytic activity
GO:0016887	0.97	ATPase activity
GO:0022857	0.95	transmembrane transporter activity
GO:0044769	0.94	ATPase activity, coupled to transmembrane movement of ions, rotational mechanism
GO:0019829	0.94	cation-transporting ATPase activity
GO:0015078	0.94	hydrogen ion transmembrane transporter activity
GO:0046933	0.93	proton-transporting ATP synthase activity, rotational mechanism
GO:1901363	0.74	heterocyclic compound binding
GO:0097159	0.74	organic cyclic compound binding
GO:0000166	0.62	nucleotide binding
GO:0035639	0.61	purine ribonucleoside triphosphate binding
GO:0032555	0.61	purine ribonucleotide binding
GO:0005524	0.60	ATP binding
GO:0046961	0.53	proton-transporting ATPase activity, rotational mechanism

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:0044237	0.98	cellular metabolic process
GO:0071704	0.97	organic substance metabolic process
GO:0044238	0.97	primary metabolic process
GO:0034641	0.96	cellular nitrogen compound metabolic process
GO:1901564	0.95	organonitrogen compound metabolic process
GO:0006139	0.94	nucleobase-containing compound metabolic process
GO:0044281	0.93	small molecule metabolic process
GO:1901576	0.92	organic substance biosynthetic process
GO:0044271	0.92	cellular nitrogen compound biosynthetic process
GO:0019693	0.92	ribose phosphate metabolic process
GO:0009117	0.92	nucleotide metabolic process
GO:1901566	0.91	organonitrogen compound biosynthetic process
GO:0046034	0.91	ATP metabolic process
GO:0006810	0.91	transport
GO:1901137	0.89	carbohydrate derivative biosynthetic process
GO:0034654	0.89	nucleobase-containing compound biosynthetic process
GO:1902600	0.88	hydrogen ion transmembrane transport
GO:0006754	0.88	ATP biosynthetic process
GO:0015986	0.87	ATP synthesis coupled proton transport
GO:0042777	0.60	plasma membrane ATP synthesis coupled proton transport

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:0044425	1.00	membrane part
GO:0044424	1.00	intracellular part
GO:0032991	0.98	macromolecular complex
GO:0098796	0.97	membrane protein complex
GO:0044444	0.94	cytoplasmic part
GO:0045261	0.88	proton-transporting ATP synthase complex, catalytic core F(1)
GO:0044446	0.85	intracellular organelle part
GO:0043226	0.76	organelle
GO:0016020	0.76	membrane
GO:0043229	0.75	intracellular organelle
GO:0043227	0.75	membrane-bounded organelle
GO:0043231	0.74	intracellular membrane-bounded organelle
GO:0044429	0.70	mitochondrial part
GO:0098798	0.69	mitochondrial protein complex
GO:0098800	0.68	inner mitochondrial membrane protein complex
GO:0045259	0.61	proton-transporting ATP synthase complex
GO:0005739	0.59	mitochondrion
GO:0005753	0.58	mitochondrial proton-transporting ATP synthase complex

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	1hm9B	0.391	5.77	0.047	0.629	2.3.1.157 2.7.7.23	113
2	0.060	2nyaF	0.369	5.79	0.054	0.586	1.7.99.4	NA
3	0.060	1h0hA	0.369	5.70	0.041	0.586	1.2.1.2	NA
4	0.060	3dwcB	0.378	5.53	0.047	0.564	3.4.17.19	NA
5	0.060	3g61A	0.434	5.60	0.028	0.650	3.6.3.44	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	0.05	2hldY	0.669	1.48	0.315	0.704	0.92	III	Download	131,132,133,134,139,141,142
2	0.01	2hydA	0.430	5.38	0.030	0.636	0.59	NA	Download	88,89,230,231
3	0.01	1jqkB	0.418	5.38	0.038	0.611	0.55	SF4	Download	82,88,90
4	0.01	2yl4A	0.433	5.53	0.043	0.650	0.56	14Y	Download	89,93,96,112
5	0.01	2w6dB	0.443	5.26	0.077	0.664	0.56	CPL	Download	81,82,83,84,115,116

	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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