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COFACTOR result for job id 76396

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>76396 (192 residues)
MSSKLIAIIIFIVIYLIFLLITFILTYFYQIKNKDFIEFNKKYLNEWNKYKFDNKNSSLN
EIDFKYQLPENEIGLFQKELLISGINQKIKDYKDYFDDDYLVLKKSLSLYQTTSYDFKQV
KLYLTNLHLVIDDNNQFYKYKIIEIKSCSICVIRDKNLLQKGCVLKTNDQSLTILGDVFL
LVLSIKKLKKEF

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	4gxbA	0.51	4.53	0.087	0.724	Download
2	3pvlA	0.50	3.83	0.074	0.672	Download
3	5xbfA	0.48	4.41	0.048	0.688	Download
4	4ekuA	0.48	3.97	0.107	0.635	Download
5	3zdtA	0.48	4.22	0.074	0.646	Download
6	6b3yA	0.48	4.14	0.099	0.641	Download
7	2j0kB	0.48	3.77	0.086	0.620	Download
8	5ixdA	0.47	4.19	0.104	0.641	Download
9	3ivfA	0.41	3.43	0.083	0.516	Download
10	1uf2B1	0.37	5.50	0.035	0.641	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	0.97	catalytic activity
GO:0004672	0.85	protein kinase activity
GO:0036122	0.84	BMP binding
GO:0004675	0.84	transmembrane receptor protein serine/threonine kinase activity
GO:0017111	0.80	nucleoside-triphosphatase activity
GO:0022857	0.55	transmembrane transporter activity
GO:0042626	0.54	ATPase activity, coupled to transmembrane movement of substances
GO:0022890	0.51	inorganic cation transmembrane transporter activity
GO:0019829	0.51	cation-transporting ATPase activity
GO:0015318	0.51	inorganic solute uptake transmembrane transporter 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:0065007	0.91	biological regulation
GO:0050789	0.88	regulation of biological process
GO:0050794	0.87	regulation of cellular process
GO:0051239	0.86	regulation of multicellular organismal process
GO:0050896	0.86	response to stimulus
GO:0032502	0.86	developmental process
GO:0007165	0.86	signal transduction
GO:0050793	0.85	regulation of developmental process
GO:0048856	0.85	anatomical structure development
GO:0048583	0.85	regulation of response to stimulus
GO:0048519	0.85	negative regulation of biological process
GO:0048518	0.85	positive regulation of biological process
GO:0032501	0.85	multicellular organismal process
GO:0023051	0.85	regulation of signaling
GO:0006950	0.85	response to stress
GO:0050832	0.84	defense response to fungus
GO:0045944	0.84	positive regulation of transcription from RNA polymerase II promoter
GO:0045087	0.84	innate immune response
GO:0040024	0.84	dauer larval development
GO:0040018	0.84	positive regulation of multicellular organism growth
GO:0030514	0.84	negative regulation of BMP signaling pathway
GO:0030513	0.84	positive regulation of BMP signaling pathway
GO:0030509	0.84	BMP signaling pathway
GO:0018991	0.84	oviposition

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:0044464	1.00	cell part
GO:0044424	0.98	intracellular part
GO:0016020	0.89	membrane
GO:0005886	0.86	plasma membrane
GO:0043229	0.77	intracellular organelle
GO:0043232	0.52	intracellular non-membrane-bounded organelle
GO:0043227	0.52	membrane-bounded organelle
GO:0043231	0.51	intracellular membrane-bounded organelle
GO:0005856	0.51	cytoskeleton

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	1bwnA	0.417	2.95	0.112	0.510	2.7.10.2	NA
2	0.060	2j0mA	0.470	4.03	0.078	0.630	2.7.10.2	NA
3	0.060	2j0kB	0.475	3.77	0.086	0.620	2.7.10.2	NA
4	0.060	2ac1A	0.412	5.34	0.070	0.698	3.2.1.26	91
5	0.060	2vlcA	0.429	4.88	0.025	0.682	3.2.2.22	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:

Click to view	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	1nu2A	0.435	3.40	0.079	0.542	0.13	III	Download	59,60,62,63,64

	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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