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COFACTOR result for job id 76664

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>76664 (101 residues)
MLHTAFISNILANYLGAMSIILPNILAVDGNIKYIGAGLASVGILGTGVGQGLIGQGACL
AIGRNPEMASKVTSTMIVSAGISESGAIYSLVIAILLIFVV

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	4bemJ	0.87	1.69	0.248	0.990	Download
2	3j9tY	0.82	1.77	0.216	0.960	Download
3	5tj5D	0.82	1.81	0.186	0.960	Download
4	2cydA	0.80	2.02	0.196	0.960	Download
5	3mk7A	0.74	2.52	0.079	1.000	Download
6	5tj5B	0.74	1.80	0.159	0.861	Download
7	4xydA	0.73	2.49	0.081	0.980	Download
8	3o0rB3	0.72	2.55	0.091	0.980	Download
9	2wieA	0.67	1.52	0.347	0.743	Download
10	1ycev	0.66	1.71	0.341	0.743	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:0005215	1.00	transporter activity
GO:0016787	0.99	hydrolase activity
GO:0044769	0.98	ATPase activity, coupled to transmembrane movement of ions, rotational mechanism
GO:0019829	0.98	cation-transporting ATPase activity
GO:0015078	0.98	hydrogen ion transmembrane transporter activity
GO:0046933	0.90	proton-transporting ATP synthase activity, rotational mechanism
GO:0008289	0.78	lipid binding
GO:0046961	0.64	proton-transporting ATPase activity, rotational mechanism
GO:0015318	0.53	inorganic solute uptake transmembrane transporter 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:

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[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	1.00	cellular process
GO:0044699	0.99	single-organism process
GO:0044763	0.98	single-organism cellular process
GO:0044237	0.98	cellular metabolic process
GO:1901564	0.97	organonitrogen compound metabolic process
GO:0044281	0.97	small molecule metabolic process
GO:0006139	0.97	nucleobase-containing compound metabolic process
GO:1901566	0.96	organonitrogen compound biosynthetic process
GO:1901293	0.96	nucleoside phosphate biosynthetic process
GO:1901137	0.96	carbohydrate derivative biosynthetic process
GO:0046034	0.96	ATP metabolic process
GO:0015672	0.96	monovalent inorganic cation transport
GO:0015986	0.95	ATP synthesis coupled proton transport
GO:0015991	0.87	ATP hydrolysis coupled proton transport
GO:0065007	0.60	biological regulation
GO:0065008	0.56	regulation of biological quality
GO:0098771	0.53	inorganic ion homeostasis
GO:0055080	0.53	cation homeostasis
GO:0030003	0.52	cellular cation homeostasis
GO:0006885	0.52	regulation of pH
GO:0051453	0.51	regulation of intracellular pH
GO:0045851	0.51	pH reduction
GO:0017144	0.51	drug metabolic process
GO:0051452	0.50	intracellular pH reduction

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:0044425	1.00	membrane part
GO:0098796	0.94	membrane protein complex
GO:0016020	0.86	membrane
GO:0044446	0.85	intracellular organelle part
GO:0016021	0.85	integral component of membrane
GO:0033177	0.80	proton-transporting two-sector ATPase complex, proton-transporting domain
GO:0043226	0.68	organelle
GO:0043229	0.67	intracellular organelle
GO:0043227	0.67	membrane-bounded organelle
GO:0043231	0.66	intracellular membrane-bounded organelle
GO:0045263	0.56	proton-transporting ATP synthase complex, coupling factor F(o)
GO:0005886	0.55	plasma 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	0.568	2w5jA	0.663	1.86	0.286	0.743	3.6.3.14	84
2	0.187	1a91A	0.617	1.94	0.120	0.723	3.6.3.14	NA
3	0.169	2bl2A	0.799	2.03	0.196	0.960	3.6.3.14	14,84
4	0.153	2wieA	0.676	1.76	0.342	0.752	3.6.3.14	84
5	0.119	1urfA	0.480	2.69	0.058	0.634	2.7.11.13	45,93

	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	0.06	2xqtD	0.678	1.76	0.342	0.752	1.21	CVM	Download	46,50,53
2	0.06	2wieD	0.675	1.78	0.342	0.752	0.98	CVM	Download	31,32,35,36,39
3	0.04	1ow7B	0.662	2.93	0.085	0.931	0.87	III	Download	12,15,16,19,22,38,41,45,48,49
4	0.02	1ow6A	0.651	2.91	0.043	0.931	0.99	III	Download	43,46,47,50,53

	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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