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COFACTOR result for job id 76285

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>76285 (450 residues)
MNVNDILKELKLSLMANKNIDESVYNDYIKTINIHKKGFSDYIVVVKSQFGLLAIKQFRQ
TIENEIKNILKEPVNISFTYEQEYKKQLEKDELINKDHSDIITKKVKKTNENTFENFVIG
ASNEQAFIAVQTVSKNPGISYNPLFIYGESGMGKTHLLKAAKNYIESNFSDLKVSYMSGD
EFARKAVDILQKTHKEIEQFKNEVCQNDVLIIDDVQFLSYKEKTNEIFFTIFNNFIENDK
QLFFSSDKSPELLNGFDNRLITRFNMGLSIAIQKLDNKTATAIIKKEIKNQNIKSEVTSE
AINFISNYYSDDVRKIKGSVSRLNFWSQQNPEEKIITIEIISDLFRDIPTSKLGILNVKK
IKEVVSEKYGISVNAIDGKARSKSIVTARHIAMFLTKEILNHTLAQIGEEFGGRDHTTVI
NAERKIETMLKKDKQLKKTVDILKNKILTK

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	1l8qA	0.69	1.16	0.371	0.700	Download
2	5e7pA	0.55	4.84	0.105	0.709	Download
3	1sxjD	0.51	4.25	0.092	0.631	Download
4	1sxjC	0.51	4.47	0.111	0.636	Download
5	6e101	0.51	4.75	0.089	0.653	Download
6	6mdmB	0.51	5.07	0.071	0.673	Download
7	1sxjA	0.51	4.86	0.113	0.642	Download
8	1r6bX	0.50	5.24	0.084	0.664	Download
9	2z4sA	0.50	1.92	0.331	0.531	Download
10	5vy9A	0.50	5.45	0.084	0.687	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:0043565	0.98	sequence-specific DNA binding
GO:0003824	0.68	catalytic activity
GO:0003690	0.66	double-stranded DNA binding
GO:0003688	0.65	DNA replication origin binding
GO:0036094	0.64	small molecule binding
GO:0000166	0.63	nucleotide binding
GO:0035639	0.62	purine ribonucleoside triphosphate binding
GO:0032555	0.62	purine ribonucleotide binding
GO:0005524	0.61	ATP binding

Download full result of the above consensus prediction.

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(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:0006259	1.00	DNA metabolic process
GO:0006270	0.98	DNA replication initiation
GO:0065007	0.69	biological regulation
GO:0050794	0.68	regulation of cellular process
GO:0080090	0.67	regulation of primary metabolic process
GO:0060255	0.67	regulation of macromolecule metabolic process
GO:0051171	0.67	regulation of nitrogen compound metabolic process
GO:0031323	0.67	regulation of cellular metabolic process
GO:2000112	0.66	regulation of cellular macromolecule biosynthetic process
GO:0019219	0.66	regulation of nucleobase-containing compound metabolic process
GO:0051052	0.65	regulation of DNA metabolic process
GO:0006275	0.64	regulation of DNA replication

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	0.98	intracellular part
GO:0016020	0.94	membrane
GO:0005886	0.93	plasma membrane
GO:0044444	0.82	cytoplasmic part
GO:0005737	0.75	cytoplasm
GO:0005829	0.61	cytosol

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	0.260	1ixsB	0.482	4.62	0.116	0.613	3.6.4.12	314
2	0.213	1in5A	0.456	4.25	0.118	0.553	3.6.4.12	314
3	0.060	2wwyA	0.373	5.75	0.066	0.516	3.6.4.12	NA
4	0.060	2jfdA	0.242	6.50	0.050	0.367	2.3.1.85	NA
5	0.060	3glfG	0.474	5.04	0.086	0.609	2.7.7.7	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	0.50	1l8qA	0.695	1.20	0.370	0.709	1.59	ADP	Download	116,117,118,123,151,152,153,154,155,156,275,283,313

	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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