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COFACTOR result for job id 76582

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

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>76582 (73 residues)
MAIYNQIVKELKSRGAKGNITKDSEFKSLGLDSLDLMDMVVTLEEKLNIRISDDQLLSLR
TIDDLLKVIEELQ

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	1x3oA	0.90	1.10	0.247	1.000	Download
2	2faeA	0.90	1.31	0.260	1.000	Download
3	3gzlA	0.90	1.15	0.342	1.000	Download
4	2qnwA	0.88	1.15	0.260	1.000	Download
5	4zxhA	0.88	1.20	0.192	1.000	Download
6	4zjbG	0.88	1.24	0.329	1.000	Download
7	2fvfA	0.88	1.34	0.342	1.000	Download
8	2cgqA	0.86	1.30	0.236	0.986	Download
9	2ehtA	0.86	1.23	0.236	0.986	Download
10	2cq8A	0.86	1.26	0.110	1.000	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:0000036	0.85	ACP phosphopantetheine attachment site binding involved in fatty acid biosynthetic process
GO:0003700	0.75	transcription factor activity, sequence-specific DNA binding
GO:1901363	0.70	heterocyclic compound binding
GO:0097159	0.70	organic cyclic compound binding
GO:0003677	0.69	DNA binding
GO:0001217	0.66	bacterial-type RNA polymerase transcriptional repressor activity, sequence-specific DNA binding
GO:0000976	0.66	transcription regulatory region sequence-specific DNA binding
GO:0003824	0.50	catalytic activity

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:0008152	0.97	metabolic process
GO:0044699	0.96	single-organism process
GO:0044710	0.95	single-organism metabolic process
GO:0009987	0.95	cellular process
GO:0071704	0.93	organic substance metabolic process
GO:0044237	0.92	cellular metabolic process
GO:0009058	0.92	biosynthetic process
GO:1901576	0.91	organic substance biosynthetic process
GO:0044711	0.91	single-organism biosynthetic process
GO:0044763	0.90	single-organism cellular process
GO:0044249	0.90	cellular biosynthetic process
GO:0044238	0.88	primary metabolic process
GO:0044281	0.87	small molecule metabolic process
GO:0044283	0.86	small molecule biosynthetic process
GO:0008610	0.86	lipid biosynthetic process
GO:0060255	0.85	regulation of macromolecule metabolic process
GO:0019219	0.85	regulation of nucleobase-containing compound metabolic process
GO:0006082	0.85	organic acid metabolic process
GO:0006633	0.84	fatty acid biosynthetic process
GO:0006355	0.84	regulation of transcription, DNA-templated
GO:0045892	0.72	negative regulation of transcription, DNA-templated
GO:0050896	0.56	response to stimulus

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:0005737	1.00	cytoplasm
GO:0032991	0.89	macromolecular complex
GO:0044444	0.85	cytoplasmic part
GO:0032993	0.84	protein-DNA complex
GO:0043229	0.61	intracellular organelle
GO:0043231	0.54	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	0.139	1hqbA	0.802	1.88	0.151	1.000	6.1.1.13	NA
2	0.118	2cg5B	0.590	2.73	0.197	0.904	3.1.2.14	NA
3	0.060	2pffD	0.624	2.50	0.000	0.931	2.3.1.86	NA
4	0.060	3e9iA	0.597	2.93	0.100	0.945	6.1.1.6	NA
5	0.060	3hrkA	0.629	2.63	0.130	0.945	6.1.1.21	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	0.40	2kooA	0.786	1.66	0.315	0.986	1.07	SXH	Download	26,27,33,37,38,53,56,57,59,60,61,65
	2	0.40	2facB	0.887	1.36	0.260	1.000	1.21	PM4	Download	26,33,36,40,43,44,49,51,56,59,68,69

	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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