[back]

COFACTOR result for job id 76570

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

User Input

>76570 (404 residues)
MNYNNKKTLKDIDVKNKTVLVRVDFNVPIQSGVITDDNRIIAALPTINYLLENDAKIVLF
SHLSRIKSKEDKLKKSLAPVAKRLEELLNKQVKFINQTRGQELEQAISSLQSKEIILVEN
TRFEDVLDDQVVKYESKNNYELGKYWASLGEVFVNDAFGTAHRAHASNVGIASNIKVSAI
GFLVEKELKMLSQAVNEPKKPFIAILGGAKVSDKIGVIENLLPKVDKLLIGGGMSYTFLK
ALGKTIGKSLLEEDKIDLAKHYLEIGKDKIVVPVDTACAKEFADVSPTIFEGNIPDEWDG
LDAGPKTIELFKQEIKKAKTIVWNGPVGVFEFKNFENGTKSVCQAIAEQTQNGAFTLIGG
GDSASAAINMGFKDKFSWISTGGGASLEFMEGKELLGISAIQDK

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	1vpeA	0.96	0.61	0.579	0.965	Download
2	2cunA	0.88	2.10	0.364	0.946	Download
3	16pkA	0.86	2.69	0.452	0.970	Download
4	1kf0A	0.86	3.16	0.439	0.988	Download
5	3q3vA	0.85	2.31	0.468	0.936	Download
6	1phpA	0.83	3.01	0.539	0.960	Download
7	4dg5A	0.83	3.09	0.553	0.958	Download
8	1v6sA	0.82	3.06	0.481	0.953	Download
9	3zlbA	0.81	3.49	0.571	0.970	Download
10	1ltkC	0.80	3.69	0.458	0.968	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:0004618	0.99	phosphoglycerate kinase activity
GO:0000166	0.95	nucleotide binding
GO:0035639	0.94	purine ribonucleoside triphosphate binding
GO:0032559	0.94	adenyl ribonucleotide binding
GO:0032550	0.94	purine ribonucleoside binding
GO:0005524	0.93	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	0.98	cellular process
GO:0008152	0.97	metabolic process
GO:0044237	0.96	cellular metabolic process
GO:0071704	0.91	organic substance metabolic process
GO:0006796	0.90	phosphate-containing compound metabolic process
GO:0044238	0.89	primary metabolic process
GO:0016310	0.88	phosphorylation
GO:0006807	0.88	nitrogen compound metabolic process
GO:0034641	0.86	cellular nitrogen compound metabolic process
GO:1901564	0.84	organonitrogen compound metabolic process
GO:0006139	0.83	nucleobase-containing compound metabolic process
GO:0044281	0.80	small molecule metabolic process
GO:1901135	0.77	carbohydrate derivative metabolic process
GO:0055086	0.77	nucleobase-containing small molecule metabolic process
GO:0019752	0.77	carboxylic acid metabolic process
GO:0019637	0.77	organophosphate metabolic process
GO:1901575	0.76	organic substance catabolic process
GO:0019693	0.76	ribose phosphate metabolic process
GO:0009117	0.76	nucleotide metabolic process
GO:0009167	0.75	purine ribonucleoside monophosphate metabolic process
GO:0009150	0.75	purine ribonucleotide metabolic process
GO:0006732	0.75	coenzyme metabolic process
GO:0005975	0.75	carbohydrate metabolic process
GO:0046496	0.74	nicotinamide nucleotide metabolic process
GO:0046034	0.74	ATP metabolic process
GO:0016052	0.74	carbohydrate catabolic process
GO:0009185	0.74	ribonucleoside diphosphate metabolic process
GO:0006165	0.74	nucleoside diphosphate phosphorylation
GO:0006091	0.74	generation of precursor metabolites and energy
GO:0006090	0.74	pyruvate metabolic process
GO:0006096	0.73	glycolytic process
GO:1901576	0.67	organic substance biosynthetic process
GO:0050896	0.56	response to stimulus
GO:0044283	0.53	small molecule biosynthetic process
GO:0065007	0.51	biological regulation
GO:0005996	0.51	monosaccharide metabolic process
GO:0019318	0.50	hexose metabolic process
GO:0016051	0.50	carbohydrate biosynthetic 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:0044424	1.00	intracellular part
GO:0044444	0.89	cytoplasmic part
GO:0005737	0.78	cytoplasm
GO:0043226	0.71	organelle
GO:0043227	0.66	membrane-bounded organelle
GO:0005829	0.64	cytosol
GO:0043229	0.63	intracellular organelle
GO:0043231	0.59	intracellular 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	0.596	3c39A	0.858	2.83	0.439	0.955	2.7.2.3	39,210,384
2	0.549	1phpA	0.832	3.01	0.539	0.960	2.7.2.3	39,210,361,384
3	0.539	1v6sA	0.824	3.06	0.481	0.953	2.7.2.3	39,210,361,384
4	0.461	2cunA	0.883	2.10	0.364	0.946	2.7.2.3	39,361,384
5	0.185	1vpeA	0.959	0.61	0.579	0.965	2.7.2.3	39,210,361,384

	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	0.54	2wzbA	0.887	2.43	0.435	0.973	1.46	UUU	Download	24,26,39,62,65,122,159,163,214,360,361,383,384
2	0.37	13pkD	0.927	1.53	0.456	0.965	1.29	PO4	Download	39,360,361,383
3	0.31	2wzcA	0.883	2.48	0.433	0.973	1.22	UUU	Download	24,26,39,62,65,122,159,162,163,208,209,210,214,232,233,324,326,328,329,331,360,361,362,363,383,384
4	0.27	2x14A	0.886	2.42	0.435	0.973	1.01	3PG	Download	24,26,40,62,122,159,162,163
5	0.07	2cunA	0.883	2.10	0.364	0.946	0.98	MPD	Download	38,39,361,381

	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).

[back]