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COFACTOR result for job id 76375

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

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>76375 (297 residues)
MKKGKMIIISGPSGVGKGSVNGELLQNPDLRLKYSVSMTTRKPRNGEINGVNYFFVSNEE
FAKAIVNDELIEYAHFVGNSYGTPRKYVEQELKKGNNVILEIEVDGATQVLNKEANVLSI
FLMPPNLTELANRIRGRQTEDEEKIKARLDKALLEIPLKHNYQYVIENDNVANAVAKITD
VLHLEGLTDIKTPTVYERLEQIVEQIVKEKYMYFVNNWETNVKLLAKNEEEKNKAKNFDA
ETYLIKLLTKKVYHKVLGHGDFSKLLDKDFVDFKIQKLMFKINFFSVEQKHYNNDEF

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	3tr0A	0.62	1.07	0.322	0.633	Download
2	6mfuA	0.61	2.85	0.327	0.680	Download
3	2qorA	0.59	1.87	0.280	0.626	Download
4	1lvgA	0.59	1.84	0.326	0.623	Download
5	1ex7A	0.57	1.89	0.399	0.616	Download
6	1z6gA	0.55	2.56	0.280	0.626	Download
7	3lncA	0.55	1.47	0.351	0.572	Download
8	5a4jA	0.53	5.03	0.097	0.748	Download
9	1eg7A	0.53	5.06	0.074	0.751	Download
10	3epjA3	0.53	3.66	0.138	0.650	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	1.00	catalytic activity
GO:0016740	0.99	transferase activity
GO:0004385	0.98	guanylate kinase activity
GO:1901363	0.86	heterocyclic compound binding
GO:0097159	0.86	organic cyclic compound binding
GO:0035639	0.83	purine ribonucleoside triphosphate binding
GO:0032559	0.83	adenyl ribonucleotide binding
GO:0005524	0.82	ATP binding
GO:0005102	0.56	receptor binding
GO:0035255	0.51	ionotropic glutamate receptor 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:

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[0.9,1.0]

Biological Process (BP)

GO term	Cscore^GO	Name
GO:0009987	1.00	cellular process
GO:0044763	0.99	single-organism cellular process
GO:0071704	0.97	organic substance metabolic process
GO:0044238	0.97	primary metabolic process
GO:0044237	0.97	cellular metabolic process
GO:0006807	0.96	nitrogen compound metabolic process
GO:0006139	0.95	nucleobase-containing compound metabolic process
GO:1901564	0.94	organonitrogen compound metabolic process
GO:0044281	0.94	small molecule metabolic process
GO:0055086	0.93	nucleobase-containing small molecule metabolic process
GO:0019637	0.93	organophosphate metabolic process
GO:0006796	0.93	phosphate-containing compound metabolic process
GO:0009117	0.92	nucleotide metabolic process
GO:0019693	0.91	ribose phosphate metabolic process
GO:0006163	0.91	purine nucleotide metabolic process
GO:1901068	0.90	guanosine-containing compound metabolic process
GO:0009167	0.90	purine ribonucleoside monophosphate metabolic process
GO:0009150	0.90	purine ribonucleotide metabolic process
GO:0046037	0.89	GMP metabolic process
GO:0051179	0.80	localization
GO:0016043	0.75	cellular component organization
GO:0032502	0.70	developmental process
GO:1902578	0.67	single-organism localization
GO:0008104	0.63	protein localization
GO:0048856	0.61	anatomical structure development
GO:1901576	0.57	organic substance biosynthetic process
GO:0007163	0.57	establishment or maintenance of cell polarity
GO:0044249	0.56	cellular biosynthetic process
GO:0045197	0.55	establishment or maintenance of epithelial cell apical/basal polarity
GO:0007154	0.55	cell communication
GO:0007267	0.54	cell-cell signaling
GO:0044271	0.52	cellular nitrogen compound biosynthetic process
GO:0051641	0.51	cellular localization
GO:0034613	0.50	cellular protein localization

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:0044424	1.00	intracellular part
GO:0044444	0.93	cytoplasmic part
GO:0043226	0.83	organelle
GO:0005829	0.83	cytosol
GO:0044425	0.80	membrane part
GO:0043229	0.80	intracellular organelle
GO:0016020	0.79	membrane
GO:0044459	0.78	plasma membrane part
GO:0005737	0.78	cytoplasm
GO:0032991	0.74	macromolecular complex
GO:0098590	0.68	plasma membrane region
GO:0097458	0.63	neuron part
GO:0044456	0.62	synapse part
GO:0043232	0.61	intracellular non-membrane-bounded organelle
GO:0043234	0.59	protein complex
GO:0098796	0.58	membrane protein complex
GO:0097060	0.58	synaptic membrane
GO:0098797	0.57	plasma membrane protein complex
GO:1902495	0.56	transmembrane transporter complex
GO:0014069	0.56	postsynaptic density
GO:0045211	0.55	postsynaptic membrane
GO:0016323	0.55	basolateral plasma membrane
GO:0008328	0.55	ionotropic glutamate receptor complex
GO:0043227	0.50	membrane-bounded organelle

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	0.421	2j41D	0.518	2.13	0.427	0.556	2.7.4.8	13,15,17,53,74,81,102,109,162
2	0.413	2an9A	0.602	2.04	0.363	0.643	2.7.4.8	17,40,50,54
3	0.284	1z6gA	0.554	2.56	0.280	0.626	2.7.4.8	14,16,18,101
4	0.278	1znyA	0.477	3.76	0.301	0.589	2.7.4.8	16,72,124,155,165
5	0.066	1qf9A	0.452	3.07	0.110	0.535	2.7.4.14	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	0.59	2an9B	0.605	1.99	0.363	0.643	1.37	GDP	Download	37,41,44,53,72,74,81,82,101,102,103,106
2	0.17	1lvgA	0.587	1.84	0.326	0.623	1.40	ADP	Download	14,15,16,17,18,19,133,137,168,169,171
3	0.16	2qorA	0.600	1.93	0.281	0.636	1.55	POP	Download	14,15,16,17,18,136

	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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