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COFACTOR result for job id 76551

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

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>76551 (133 residues)
MLFGTYEHCMDAKQRLTLPAKLRNKLSNPIYLTKGYDADLEIWSKDDFLLQIKEILNQQN
DQKDIRNIERIIWSNTVEIDIDNLGRIKIPYNLIQNLNIEKDVFILGLGNRLEIWSKNKY
NQHKNKFIKNINS

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	1n0eB	0.97	1.11	0.331	1.000	Download
2	4hynA	0.53	3.85	0.115	0.767	Download
3	3qtaA	0.51	3.99	0.043	0.774	Download
4	1xkrA	0.50	4.19	0.043	0.767	Download
5	4w8yA	0.50	4.15	0.052	0.782	Download
6	2q8gA	0.49	4.21	0.064	0.752	Download
7	3ty5A	0.49	4.66	0.047	0.804	Download
8	1y8pA	0.47	4.18	0.064	0.737	Download
9	1xkoB	0.45	3.91	0.096	0.647	Download
10	3crlB1	0.41	4.55	0.079	0.647	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:0003700	1.00	transcription factor activity, sequence-specific DNA binding
GO:0000976	1.00	transcription regulatory region sequence-specific DNA binding
GO:0003824	0.72	catalytic activity

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:

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[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	0.78	cellular process
GO:0065007	0.72	biological regulation
GO:0050789	0.72	regulation of biological process
GO:0050794	0.71	regulation of cellular process
GO:2000112	0.70	regulation of cellular macromolecule biosynthetic process
GO:0080090	0.70	regulation of primary metabolic process
GO:0051171	0.70	regulation of nitrogen compound metabolic process
GO:0010468	0.70	regulation of gene expression
GO:0006355	0.69	regulation of transcription, DNA-templated
GO:0040007	0.57	growth
GO:0071704	0.54	organic substance metabolic process
GO:0044237	0.53	cellular metabolic process
GO:0044238	0.51	primary 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	0.85	intracellular part
GO:0044444	0.56	cytoplasmic part
GO:0016020	0.48	membrane
GO:0005737	0.48	cytoplasm
GO:0005886	0.43	plasma membrane
GO:0042597	0.33	periplasmic space
GO:0009295	0.33	nucleoid

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	0.060	2dhtA	0.451	4.84	0.116	0.820	1.1.1.42	82
2	0.060	2zdxA	0.477	4.32	0.063	0.744	2.7.11.2	NA
3	0.060	1ug9A	0.452	5.04	0.052	0.820	3.2.1.70	NA
4	0.060	2pflA	0.449	4.72	0.051	0.752	2.3.1.54	NA
5	0.060	1cnzA	0.453	4.77	0.031	0.804	1.1.1.85	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:

Rank	Cscore^LB	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	BS-score	Lig. Name	Download Complex	Predicted binding site residues
1	0.22	2zkjA	0.469	4.39	0.072	0.752	0.24	UUU	Download	9,19,30
2	0.21	2bu8A	0.476	4.30	0.080	0.752	0.31	ADP	Download	31,42,82,83,84,112
3	0.01	3crlA	0.470	4.33	0.071	0.752	0.16	ANP	Download	22,25,26,86,107,108
4	0.01	2e0aA	0.483	4.05	0.073	0.737	0.19	ANP	Download	23,89,107
5	0.01	1hqsB	0.471	4.89	0.041	0.880	0.19	CIT	Download	10,17,19,82
6	0.01	2bu2A	0.474	4.21	0.080	0.744	0.25	TF1	Download	19,22,23
7	0.01	2qfwF	0.473	4.64	0.040	0.827	0.13	ICT	Download	4,28,87
8	0.01	2q8gA	0.492	4.21	0.064	0.752	0.34	AZX	Download	21,22,111
9	0.01	2zdyB	0.468	4.31	0.061	0.752	0.26	ADP	Download	85,87,112
10	0.01	3ty3B	0.476	4.96	0.080	0.887	0.13	GGG	Download	86,87,89,107

	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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