[back]

COFACTOR result for job id 76622

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

User Input

>76622 (288 residues)
MVILDGKLVSKQIKETLKQQIDTYLNKNYKKPKLVVILIGNDPASELYVSNKIKACNLVG
IESVLLRFDQNITSEILSDQINQLNNDNSVDAILLQLPLPKHLNEQEFLQAIDPLKDVDG
FHYINQGKMLEGYDTIYPCTPIGIINLLKAYNIDVRSKDITIIGTSNIVGKPLAIMLSNM
GATISMCNKNTKSLKKYTKRSDIVISATGKQALIKKDMIKKNAIVIDVGIIKDPITNKIV
GDVDFENVKELCSYISPVPGGVGPMTVAMLLENTFELYKLHIKENYEN

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	6apeA	0.98	0.48	0.449	0.983	Download
2	1b0aA	0.97	0.89	0.418	0.990	Download
3	3l07B	0.96	0.69	0.463	0.976	Download
4	5tc4A	0.95	1.05	0.448	0.976	Download
5	4a26A	0.95	1.39	0.386	0.990	Download
6	1diaB	0.94	1.37	0.382	0.983	Download
7	3p2oA	0.94	0.83	0.500	0.951	Download
8	2c2yA	0.93	1.12	0.390	0.962	Download
9	5zf1A	0.93	1.03	0.446	0.958	Download
10	4cjxA	0.93	1.66	0.335	0.986	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:0004488	1.00	methylenetetrahydrofolate dehydrogenase (NADP+) activity
GO:0004477	1.00	methenyltetrahydrofolate cyclohydrolase activity
GO:0016874	0.55	ligase activity
GO:0004487	0.52	methylenetetrahydrofolate dehydrogenase (NAD+) activity
GO:0016879	0.50	ligase activity, forming carbon-nitrogen bonds

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:0006730	1.00	one-carbon metabolic process
GO:0071704	0.95	organic substance metabolic process
GO:0006807	0.94	nitrogen compound metabolic process
GO:1901564	0.91	organonitrogen compound metabolic process
GO:1901360	0.91	organic cyclic compound metabolic process
GO:0046483	0.91	heterocycle metabolic process
GO:0044238	0.91	primary metabolic process
GO:0006725	0.91	cellular aromatic compound metabolic process
GO:0055114	0.90	ox.dat.gzion-reduction process
GO:0034641	0.88	cellular nitrogen compound metabolic process
GO:0006732	0.85	coenzyme metabolic process
GO:0006760	0.84	folic acid-containing compound metabolic process
GO:0006139	0.84	nucleobase-containing compound metabolic process
GO:1901576	0.83	organic substance biosynthetic process
GO:0044249	0.83	cellular biosynthetic process
GO:0035999	0.83	tetrahydrofolate interconversion
GO:1901566	0.81	organonitrogen compound biosynthetic process
GO:0044271	0.81	cellular nitrogen compound biosynthetic process
GO:0019752	0.79	carboxylic acid metabolic process
GO:1901362	0.78	organic cyclic compound biosynthetic process
GO:0019438	0.78	aromatic compound biosynthetic process
GO:0018130	0.78	heterocycle biosynthetic process
GO:0055086	0.77	nucleobase-containing small molecule metabolic process
GO:0019637	0.77	organophosphate metabolic process
GO:0006796	0.77	phosphate-containing compound metabolic process
GO:0006520	0.77	cellular amino acid metabolic process
GO:0090407	0.76	organophosphate biosynthetic process
GO:0044283	0.76	small molecule biosynthetic process
GO:0034654	0.76	nucleobase-containing compound biosynthetic process
GO:0009117	0.76	nucleotide metabolic process
GO:1901605	0.75	alpha-amino acid metabolic process
GO:0046394	0.75	carboxylic acid biosynthetic process
GO:0006164	0.75	purine nucleotide biosynthetic process
GO:1901607	0.74	alpha-amino acid biosynthetic process
GO:0009066	0.74	aspartate family amino acid metabolic process
GO:0008652	0.74	cellular amino acid biosynthetic process
GO:0009086	0.73	methionine biosynthetic process
GO:0000105	0.73	histidine 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:0005829	1.00	cytosol
GO:0043226	0.56	organelle
GO:0043229	0.55	intracellular organelle
GO:0043227	0.54	membrane-bounded organelle
GO:0043231	0.53	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	0.663	1b0aA	0.972	0.89	0.418	0.990	1.5.1.5 3.5.4.9	52
2	0.645	2c2xA	0.933	1.14	0.390	0.962	1.5.1.5 3.5.4.9	52
3	0.209	3l07B	0.964	0.69	0.463	0.976	3.5.4.9 1.5.1.5	52
4	0.203	1a4iB	0.942	1.37	0.385	0.983	1.5.1.5 3.5.4.9	52
5	0.074	3d6nB	0.618	4.03	0.183	0.799	2.1.3.2	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	0.46	3p2oB	0.947	1.04	0.507	0.972	1.45	NAD	Download	48,140,164,165,166,169,188,189,207,208,209,213,228,229,230,263,266
2	0.27	1digA	0.945	0.94	0.385	0.965	1.62	L37	Download	52,230,260,261,263,264,267
3	0.27	1diaA	0.946	0.91	0.385	0.965	1.53	L24	Download	48,51,52,96,97,259,260,263,264,267
4	0.09	1b0a0	0.972	0.89	0.418	0.990	1.47	III	Download	121,123,124,127,128,130,131,132,156,157,159,167,171,175,178,181,182,183,184,185,186,187,188,190,191,192,197

	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]