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COFACTOR result for job id 76626

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

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>76626 (485 residues)
MQDYRKKSIFEIHKDLVDKKYTVLDLTKEVLKNLKYELDSNAINYLAEIHALKQAKKIEE
NFDSNNLLSGIPYICKDNFSTKDIPTTASSKILENYIPNYSAALVDSLEKNQSILVGKSA
LDELGMGGTGLLSCNGKITNPWDKNRIVGGSSSGSAYLVAKGLVPFATGTDTGDSIRKPA
SYNGIVGFKPTYGVISRYGLLPYAPSLDTAGFFTKNVDDMAVLCDASYDDDNRDFSSTTA
DHVDFLKQIDDFSNIKTFGYISSVIESLDQEHKTHYYNLFETLKNKGYQVKALDFRQDLL
DAVLPVYLMIANSESVSTNSCLDGIKYGKRVDGNDYSEIMINSRTQGFGEIVRRRFAIGS
LVLKGENQKKYLVQAKKVRTLINRDFNNLFEQVDVLLLPPSPSIAPLIEEINNPNKKSQE
KDFIENILVLANFTGSPSITIPFFKTKNMPVGINITTKVKTDLLTLQAAKLLENIIGIKN
QIVED

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	3ip4A	0.98	0.54	0.332	0.988	Download
2	4wj3A	0.97	0.85	0.310	0.986	Download
3	3h0lA	0.96	1.12	0.324	0.979	Download
4	3kfuE	0.94	1.11	0.295	0.957	Download
5	3a2pA	0.89	2.25	0.215	0.949	Download
6	6dhvA	0.88	2.55	0.236	0.949	Download
7	1m21A	0.88	2.79	0.225	0.953	Download
8	4yj6A	0.88	2.61	0.204	0.949	Download
9	6c62A	0.88	1.95	0.253	0.917	Download
10	4gyrA	0.87	2.25	0.219	0.924	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:0016787	0.96	hydrolase activity
GO:0016810	0.95	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds
GO:0016811	0.94	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides
GO:0004040	0.87	amidase activity
GO:0016874	0.84	ligase activity
GO:0016879	0.81	ligase activity, forming carbon-nitrogen bonds
GO:1901363	0.80	heterocyclic compound binding
GO:0097159	0.80	organic cyclic compound binding
GO:0050567	0.80	glutaminyl-tRNA synthase (glutamine-hydrolyzing) activity
GO:0000166	0.77	nucleotide binding
GO:0035639	0.76	purine ribonucleoside triphosphate binding
GO:0032555	0.76	purine ribonucleotide binding
GO:0032550	0.76	purine ribonucleoside binding
GO:0030554	0.76	adenyl nucleotide binding
GO:0005524	0.75	ATP 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	0.99	cellular process
GO:0044237	0.98	cellular metabolic process
GO:0071704	0.97	organic substance metabolic process
GO:0006807	0.95	nitrogen compound metabolic process
GO:0044238	0.94	primary metabolic process
GO:0034641	0.94	cellular nitrogen compound metabolic process
GO:1901564	0.91	organonitrogen compound metabolic process
GO:0043170	0.90	macromolecule metabolic process
GO:0044249	0.87	cellular biosynthetic process
GO:1901576	0.86	organic substance biosynthetic process
GO:1901566	0.84	organonitrogen compound biosynthetic process
GO:0044260	0.84	cellular macromolecule metabolic process
GO:0043603	0.83	cellular amide metabolic process
GO:0044271	0.82	cellular nitrogen compound biosynthetic process
GO:0034645	0.81	cellular macromolecule biosynthetic process
GO:0019538	0.81	protein metabolic process
GO:0006412	0.80	translation
GO:0044281	0.76	small molecule metabolic process
GO:0044763	0.72	single-organism cellular process
GO:1901360	0.69	organic cyclic compound metabolic process
GO:0006725	0.68	cellular aromatic compound metabolic process
GO:0006082	0.67	organic acid metabolic process
GO:0046483	0.64	heterocycle metabolic process
GO:0019752	0.64	carboxylic acid metabolic process
GO:0006139	0.60	nucleobase-containing compound metabolic process
GO:0090304	0.52	nucleic acid metabolic process

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	0.99	intracellular part
GO:0044444	0.88	cytoplasmic part
GO:0032991	0.87	macromolecular complex
GO:0043229	0.86	intracellular organelle
GO:0043234	0.83	protein complex
GO:0043231	0.75	intracellular membrane-bounded organelle
GO:0030956	0.73	glutamyl-tRNA(Gln) amidotransferase complex
GO:0005739	0.51	mitochondrion
GO:0044422	0.50	organelle part

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	0.423	2gi3A	0.851	1.94	0.296	0.887	6.3.5.-	151,152,172,173,175
2	0.374	2wj2A	0.832	2.91	0.169	0.915	3.5.1.99	76,151,152,173,175
3	0.206	3a2pA	0.889	2.25	0.215	0.949	3.5.2.12	NA
4	0.060	2ckjA	0.326	7.65	0.029	0.557	1.17.1.4 1.17.3.2	NA
5	0.060	2jfdA	0.257	7.19	0.054	0.412	2.3.1.85	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	0.21	3ppmA	0.832	2.91	0.169	0.915	0.91	JG1	Download	76,78,125,126,127,151,170,172,175,201,202,208,422,429
	2	0.05	1o9p0	0.801	2.13	0.214	0.847	0.81	III	Download	92,93,96,97,98,99,100,101,103,106,107,109,110,193,198,202,205

	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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