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COFACTOR result for job id 76594

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>76594 (317 residues)
MKQFVRPEFILLKEGQDKNYGKFSVSPLERGFGITLGNAIRRTLLAATPGASVYAIKIAG
ATHEFTSIPGIIENVTKIILNIKQLVLKIDTSIYSDDEVVQLRIRSDIQGPVYAGDLDIP
AGVEILNKDLLIATISEGGVLDLVLYAKNSRGYKTFKDNKNEKNIEPGMITIDSNYSPII
KVAYSVDSAKIGRAIDLEKLELEVTTDGSITAIDAISIASRILVAHLEFFIDLNREISVL
EVIGTNQTDDKELDRTVEELDFTQRSLNCLKRAGINTLRELVSKNEDEIGSIRNLGRKSL
KEIKDKVASLGLAFRQS

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	3iydA	0.94	1.11	0.352	0.969	Download
2	6govU	0.67	1.91	0.339	0.713	Download
3	5tw1A	0.63	2.16	0.415	0.678	Download
4	3dxjB	0.62	3.13	0.340	0.722	Download
5	4noiA	0.58	3.32	0.297	0.700	Download
6	4c2mC	0.53	3.57	0.180	0.634	Download
7	3gtjC	0.52	3.87	0.152	0.634	Download
8	4qiwD	0.52	3.50	0.255	0.615	Download
9	3h0gC	0.52	3.42	0.180	0.615	Download
10	1wstA	0.25	6.87	0.035	0.451	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	0.96	catalytic activity
GO:0016772	0.91	transferase activity, transferring phosphorus-containing groups
GO:0003899	0.90	DNA-directed RNA polymerase activity
GO:1901363	0.80	heterocyclic compound binding
GO:0097159	0.80	organic cyclic compound binding
GO:0003676	0.79	nucleic acid binding
GO:0003677	0.73	DNA binding
GO:0046983	0.72	protein dimerization activity
GO:0043167	0.56	ion binding
GO:0046872	0.54	metal ion binding
GO:0008270	0.53	zinc ion binding

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	0.97	cellular process
GO:0071704	0.95	organic substance metabolic process
GO:0044237	0.95	cellular metabolic process
GO:0044238	0.94	primary metabolic process
GO:0006807	0.94	nitrogen compound metabolic process
GO:0034641	0.93	cellular nitrogen compound metabolic process
GO:0043170	0.92	macromolecule metabolic process
GO:1901576	0.90	organic substance biosynthetic process
GO:0044249	0.90	cellular biosynthetic process
GO:0044260	0.89	cellular macromolecule metabolic process
GO:0006139	0.89	nucleobase-containing compound metabolic process
GO:0044271	0.88	cellular nitrogen compound biosynthetic process
GO:0009059	0.88	macromolecule biosynthetic process
GO:0090304	0.87	nucleic acid metabolic process
GO:0034645	0.87	cellular macromolecule biosynthetic process
GO:0016070	0.86	RNA metabolic process
GO:1901362	0.85	organic cyclic compound biosynthetic process
GO:0018130	0.85	heterocycle biosynthetic process
GO:0034654	0.84	nucleobase-containing compound biosynthetic process
GO:0006351	0.83	transcription, DNA-templated
GO:0040007	0.73	growth

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:0043229	0.94	intracellular organelle
GO:0043231	0.93	intracellular membrane-bounded organelle
GO:0009536	0.87	plastid
GO:0005829	0.63	cytosol
GO:0044446	0.60	intracellular organelle part
GO:0032991	0.56	macromolecular complex
GO:0016020	0.52	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	0.374	3dxjB	0.621	3.13	0.340	0.722	2.7.7.6	36,41,45,177,182,200,223
2	0.060	1i8qA	0.317	6.36	0.042	0.524	4.2.2.1	NA
3	0.060	3b8cB	0.319	6.61	0.030	0.536	3.6.3.6	39,43,45,183,216
4	0.060	3b8cA	0.319	6.35	0.028	0.511	3.6.3.6	NA
5	0.060	1y2mB	0.408	5.43	0.038	0.603	4.3.1.24	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	0.24	1l9u0	0.638	2.53	0.386	0.700	1.29	III	Download	9,23,29,31,32,35,36,39,42,43,216,223,224,226,227,229,230
2	0.23	1ynj0	0.648	2.33	0.378	0.704	1.17	III	Download	9,25,32,34,35,36,39,40,42,43,47,151,196,200,222,223,224,226,227,228
3	0.06	2gho1	0.647	2.28	0.378	0.704	1.08	III	Download	34,38,62,71,72,182,183,186,187
4	0.06	2a69L	0.616	2.92	0.367	0.710	1.00	MG	Download	50,175,177,178,207
5	0.06	1iw7B	0.622	2.88	0.357	0.713	0.98	MG	Download	49,50,178
6	0.06	2a6h5	0.614	2.96	0.367	0.710	0.89	III	Download	46,65,77,80,83,84,152,153,155,157,175,181
7	0.01	2hgu7	0.136	4.91	0.027	0.192	1.02	III	Download	28,29,32,33,35,36,37,39,42,43,44,45
8	0.01	1ken4	0.186	5.53	0.030	0.284	0.86	III	Download	34,37,38,41

	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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